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MDE Deployment Roadmap

A complete end-to-end deployment guide for Microsoft Defender for Endpoint — covering Intune, Security Settings Management, Defender for Cloud, and the Defender portal

How to Read This Guide

This guide covers a complete Microsoft Defender for Endpoint deployment across five phases — from licensing through onboarding, security policy configuration, incident investigation, and advanced topics. Each section identifies the recommended tool for each task, explains the underlying behaviour, and includes the relevant scripts, KQL queries, and configuration steps.

Section structure

Every topic follows the same pattern: concept explanation, prerequisites, step-by-step procedure, verification, and common issues. Scripts include inline comments explaining what each line does and why.

Deployment methods covered

This guide covers all current onboarding and policy management paths: Intune (enrolled devices), Security Settings Management (non-enrolled devices via the Defender portal), Defender for Cloud (Azure and Arc-enabled servers), and Group Policy (legacy/hybrid Active Directory environments).

Where to manage policies Microsoft recommends managing endpoint security policies from the Defender portal (security.microsoft.com → Endpoints → Configuration Management → Endpoint Security Policies) or the Intune admin center. GPO-based policy management is supported but not the recommended path for new deployments.

Glossary — Key Terms

Reference definitions for the key terms and acronyms used throughout this guide.

MDE (Microsoft Defender for Endpoint)
Microsoft's security software for protecting computers and servers. It detects threats, blocks attacks, and lets security teams investigate incidents — all from a single web portal.
SENSE Service
The background Windows service that MDE installs on each computer. Its official service name is "Windows Defender Advanced Threat Protection Service." If this service is not running, the computer is not protected.
Onboarding
The process of connecting a computer to MDE so it starts sending security data to Microsoft. Until a device is onboarded, it is invisible to your security team.
NGAV (Next-Generation Antivirus)
The antivirus component of MDE. Unlike old-style antivirus that only checks known virus signatures, NGAV uses cloud intelligence and machine learning to catch brand-new threats in real time.
EDR (Endpoint Detection & Response)
The investigation layer of MDE. EDR records everything that happens on a computer — every file created, every process launched, every network connection — so analysts can reconstruct what an attacker did.
ASR (Attack Surface Reduction)
A set of rules that block specific attack techniques before they can execute. For example, one rule blocks Office applications from spawning command-line processes — a very common malware technique.
AIR (Automated Investigation & Remediation)
MDE's built-in automation that investigates alerts and, when confident, automatically removes threats without requiring a human analyst. Requires MDE Plan 2.
TVM (Threat & Vulnerability Management)
The vulnerability scanner built into MDE. It continuously checks your devices for missing patches and misconfigurations, prioritising them by real-world exploitability.
GPO (Group Policy Object)
A Windows feature that lets IT administrators push settings to many computers at once through Active Directory. Used in this guide to distribute MDE configuration to all domain-joined devices.
KQL (Kusto Query Language)
The query language used to search security data in Microsoft Defender XDR and Microsoft Sentinel. Similar to SQL but designed for large-scale log analysis. Every KQL query in this guide is explained line by line.
Network Protection
An MDE feature that blocks devices from connecting to known malicious websites and IP addresses. It works at the kernel level, meaning it catches connections before the browser even loads the page.
Tamper Protection
A lock that prevents malware (or an attacker who has gained access) from turning off Microsoft Defender. When enabled, only the Microsoft cloud can change security settings.
Passive Mode
A special state where Microsoft Defender runs on a computer that already has a third-party antivirus installed. In passive mode, Defender does not scan files for threats — but it still collects EDR telemetry so you can investigate incidents.
Live Response
A feature that lets a security analyst open a remote command line on any onboarded device — even if the user is logged off. Used for deep forensic investigation and immediate containment.
Deployment Ring
A phased rollout strategy. You deploy to a small "Ring 0" pilot group first, verify everything works, then expand to larger groups. This prevents a bad configuration from breaking every computer at once.
IoC (Indicator of Compromise)
A known-bad file hash, IP address, domain, or URL. You can upload IoCs to MDE so it automatically blocks or alerts whenever any device tries to access them.
RBAC (Role-Based Access Control)
A permission system that controls who can see or do what in the MDE portal. A Tier 1 analyst can view alerts; a Tier 2 analyst can run Live Response; only admins can change security policies.
Device Control
A feature that controls what USB devices (flash drives, printers, phones) can do on company computers. You can allow read-only access, block entirely, or require approval — all enforced by policy.
QUIC Protocol
A modern internet transport protocol used by HTTP/3. Some attack tools use QUIC to bypass traditional firewall inspection. MDE network protection can block QUIC to force connections through inspectable HTTPS.
WCF (Windows Defender Credential Guard)
A Windows feature that protects user passwords stored in memory from being stolen by malware. Recommended to enable alongside MDE for defense-in-depth.

Plan & Prerequisites

Confirm licensing, operating system compatibility, network access, and deployment ring strategy before onboarding any devices. Gaps here cause silent onboarding failures — devices that appear to complete the process but never show up in the portal.

Complete prerequisites first Onboarding scripts run silently. An attempt against an unlicensed tenant or a blocked network produces no error — the device simply never appears in the portal.

1.1 Licensing

Plans and entitlements

MDE is available as Plan 1 (NGAV, ASR, device control) or Plan 2 (adds full EDR, Threat & Vulnerability Management, Automated Investigation, and Live Response). Plan 2 is the standard for enterprise deployments and is included in Microsoft 365 E5.

License bundles that include MDE:

License BundleMDE PlanEDRTVMAIRNotes
Microsoft 365 E3 / A3 / F3Plan 1NoCore onlyNoASR, NGAV, device control included
Microsoft 365 E5 / A5 / G5Plan 2YesFullYesFull MDE P2 included
MDE Plan 1 (standalone)Plan 1NoNoNoCan add-on to M365 E3
MDE Plan 2 (standalone)Plan 2YesYesYesCan add-on to any M365
Defender for Servers P1Plan 1NoNoNoFor Azure/Arc VMs via MDC
Defender for Servers P2Plan 2YesYesYesFull P2 for servers + file integrity
How to verify your license
  1. Sign in to the Microsoft 365 Admin Center.
  2. Go to Billing → Your products.
  3. Look for any of the license names in the table above.
  4. If you see "Microsoft Defender for Endpoint Plan 2" or "Microsoft 365 E5", you are ready to proceed.

1.2 Supported Operating Systems

Coverage note

Devices running unsupported OS versions may appear to onboard successfully but will not transmit telemetry — a silent gap in coverage. Verify version support for every platform in scope before deploying.

PlatformMinimum VersionKey Notes
Windows 10Version 1709 (Fall Creators Update, build 16299) — KB4493441 required for version 1709 specificallyFull MDE Plan 2 capabilities
Windows 11All supported versionsFull MDE Plan 2 capabilities
Windows Server 2022All buildsModern unified agent — no MMA needed
Windows Server 2019All buildsModern unified agent — no MMA needed
Windows Server 2016All buildsKB5005292 required for periodic EDR sensor stack updates with the modern unified solution
Windows Server 2012 R2All builds — sensor version 10.8040.* (March 2022) or higherMust use the modern unified agent; legacy MMA method is deprecated. Note: OS extended support ended October 2023 — plan migration to a supported OS.
macOSBig Sur (11) or laterDeploy via Intune or JAMF profiles
LinuxRHEL 7.2+, Ubuntu 16.04+, SLES 12+Manual install or Ansible/Puppet
AndroidAndroid 6.0+Deploy via Intune MDM/MAM
iOS / iPadOSiOS 14.0+Deploy via Intune supervised or unsupervised

1.3 Network Connectivity — Required URLs

Connectivity requirement

MDE communicates with Microsoft's cloud services over HTTPS (port 443). Blocked URLs result in devices appearing as "inactive" in the portal after onboarding. Verify reachability on every network segment where endpoints live, including VPN-connected remote workers. Microsoft provides two connectivity models — use Streamlined for new deployments.

Streamlined connectivity (recommended for new deployments)

A single primary endpoint replaces many legacy domain-specific URLs. Supported on Windows 10 1809+, Windows 11, Windows Server 2019+, Linux, and macOS.

# ── Streamlined MDE URLs ── allow outbound on the ports listed ─────────────────

# Core MDE services — ALL telemetry, MAPS, C&C, sample submission
*.endpoint.security.microsoft.com      port 443

# Web and network protection
*.smartscreen-prod.microsoft.com       port 443
*.smartscreen.microsoft.com            port 443

# Security intelligence and antivirus definition updates
go.microsoft.com                       port 443
definitionupdates.microsoft.com        port 443

# Certificate revocation
crl.microsoft.com                      port 80
www.microsoft.com/pkiops/*             port 80
www.microsoft.com/pki/*                port 80

# Security Settings Management (SSM) — required if using non-enrolled device management
*.dm.microsoft.com                     port 443

Standard connectivity (for existing deployments or older Windows versions)

Required for Windows 10 versions prior to 1809, and for any tenant not yet migrated to streamlined. Add these in addition to the SmartScreen and CRL entries above.

# ── Standard MDE URLs — Command and Control (all regions, all platforms) ───────
# Add the group that matches your Microsoft 365 tenant region.

# United States
winatp-gw-cus.microsoft.com
winatp-gw-cus3.microsoft.com
winatp-gw-eus.microsoft.com
winatp-gw-eus3.microsoft.com

# Europe
winatp-gw-neu.microsoft.com
winatp-gw-neu3.microsoft.com
winatp-gw-weu.microsoft.com
winatp-gw-weu3.microsoft.com

# United Kingdom
winatp-gw-uks.microsoft.com
winatp-gw-ukw.microsoft.com

# Australia
winatp-gw-aue.microsoft.com
winatp-gw-aus.microsoft.com

# ── Additional standard connectivity URLs ──────────────────────────────────────
# Threat intelligence feeds
*.blob.core.windows.net                port 443

# NOTE: *.ods.opinsights.azure.com and *.oms.opinsights.azure.com are only required
# when onboarding Windows Server 2012 R2 or 2016 using the legacy MMA-based method.
# They are NOT needed for the modern unified solution or any other platform.
SSL inspection Authenticated proxies and SSL inspection/interception are not supported on MDE endpoints. Configure a bypass exception for all MDE domains in your SSL inspection policy. Anonymous proxies are supported.
How to test connectivity before deploying Download the MDE Client Analyzer from aka.ms/mdatpanalyzer. Extract the ZIP and run MDEClientAnalyzer.cmd as Administrator. It produces an HTML report showing exactly which URLs are reachable and which are blocked.

1.4 Deployment Rings

Phased rollout strategy

Deploying to a small pilot ring first limits the blast radius of misconfiguration. A policy that locks down every device simultaneously is significantly harder to recover from than one that affects five pilot machines.

Recommended ring structure for a typical enterprise deployment:

RingSizeWhoWhen to Expand
Ring 0 — Pilot5–10 devicesIT team, security team, volunteersAfter 72 hours with no critical issues
Ring 1 — Early Adopters50–200 devicesPower users, tech-savvy staffAfter 1 week with no regressions
Ring 2 — Broad DeploymentRemaining devicesAll usersAfter Ring 1 is stable
Tip: Use Active Directory OUs for rings Create three Active Directory Organizational Units: MDE-Ring0, MDE-Ring1, and MDE-Ring2. Link your MDE onboarding GPO to each OU in sequence. This gives you precise control over which devices receive the onboarding package and when.

Onboard Endpoints

Onboarding registers a device with your MDE tenant and activates the SENSE sensor, which begins streaming telemetry to the Defender portal. Until a device is onboarded it is invisible — no alerts, no timeline, no policy enforcement. MDE supports multiple deployment paths; choose based on how your devices are managed.

2.1 Choosing a Deployment Method

MethodBest ForPolicy Management After
Intune (enrolled devices)Entra ID-joined or hybrid-joined endpoints managed by Intune MDMIntune Endpoint Security policies or Defender portal (same policies, dual UI)
Security Settings ManagementDevices onboarded to MDE but not enrolled in Intune (e.g., domain-only, BYOD, Linux, macOS)Defender portal → Configuration Management → Endpoint Security Policies
Defender for Cloud (Defender for Servers)Azure VMs, Azure Arc-enabled on-premises serversDefender for Cloud environment settings; MDE policy via Intune or Defender portal
Group PolicyLegacy Active Directory environments without Intune or modern managementGPO (registry-based) — not recommended for new deployments
Script / local deploymentPilot testing, one-off machines, non-domain devicesIntune or Defender portal after onboarding
Recommended path For Intune-managed devices, deploy an EDR policy from the Intune admin center or Defender portal to onboard at scale. For everything else (non-enrolled Windows, Linux, macOS, servers), use Security Settings Management — devices register with Entra ID automatically and receive policies from the Defender portal without requiring full Intune enrollment.

2.2 Onboarding via Intune (Enrolled Devices)

How it works

Intune deploys an EDR (Endpoint Detection and Response) policy to enrolled devices. The policy configures the SENSE service and associates the device with your tenant. No package download is needed — the onboarding blob is embedded in the policy. After onboarding, the same Intune admin center or the Defender portal can manage all endpoint security policies.

  1. Connect Intune to MDE. In the Intune admin center, go to Endpoint security → Microsoft Defender for Endpoint and set Allow Microsoft Defender for Endpoint to enforce Endpoint Security Configurations to On. Save.
  2. Create an EDR policy. In the Intune admin center, go to Endpoint security → Endpoint detection and response → Create Policy. Select Platform: Windows, Profile: Endpoint detection and response.
  3. Configure onboarding. In the policy settings, set Microsoft Defender for Endpoint client configuration package type to Auto from connector (recommended — pulls the onboarding blob automatically from the MDE-Intune connector). The manual Onboard option is also available if needed.
  4. Assign to a device group. Assign the policy to your Ring 0 Entra ID device group. Most devices receive and apply the policy within a few minutes; in some cases it can take up to 24 hours. To force immediate check-in, trigger Sync from the Intune portal or from the device.

2.3 Security Settings Management (Non-Enrolled Devices)

How it works

Security Settings Management allows MDE-onboarded devices that are not enrolled in Intune to receive Intune endpoint security policies directly from the Defender portal. The device registers a synthetic Entra ID identity on onboarding, checks in with Intune every 90 minutes, and enforces assigned policies — no MDM enrollment required. This covers Windows (domain-joined or standalone), Windows Server, Linux, and macOS.

  1. Enable the enforcement scope. In the Defender portal, go to Settings → Endpoints → Configuration Management → Enforcement Scope. Enable the platforms you want to manage (Windows Client, Windows Server, Linux, macOS).
  2. Pilot on tagged devices. Start with On tagged devices and tag pilot machines with the MDE-Management device tag. This limits the initial scope.
  3. Enable the Intune connector. In the Intune admin center, go to Endpoint security → Microsoft Defender for Endpoint and set Allow Microsoft Defender for Endpoint to enforce Endpoint Security Configurations to On.
  4. Onboard devices. Use the onboarding package appropriate for each platform (script, GPO, Ansible, etc.). Once onboarded, each device appears in both the Defender portal and Intune admin center with Managed by: MDE.
  5. Create Entra ID device groups. Create dynamic groups based on deviceOSType (Windows, Windows Server, Linux, macOS) to target policies. Use managementType eq "MicrosoftSense" to target only Security Settings Management devices.
  6. Deploy endpoint security policies. From the Defender portal (Endpoints → Configuration Management → Endpoint Security Policies) or the Intune admin center (Endpoint security), create and assign policies. The same policies work for both enrolled and non-enrolled devices.
Licensing exception Security Settings Management requires at least one MDE Plan 2 user license. Access through Defender for Servers only (no user MDE license) does not grant Security Settings Management capability.
Assignment filters are not supported When targeting SSM-managed devices, policies must be assigned to device groups — assignment filters are not supported for Security Settings Management devices. Use dynamic Entra ID groups with the managementType eq "MicrosoftSense" filter to scope policies to SSM-managed devices only.

2.4 Onboarding Servers via Defender for Cloud

How it works

When you enable the Defender for Servers plan in Microsoft Defender for Cloud, MDE integration is enabled by default and the MDE sensor is automatically deployed to supported Azure VMs and Azure Arc-enabled on-premises machines. No manual onboarding package is needed. Defender for Servers Plan 2 provides the full MDE Plan 2 feature set.

  1. Enable Defender for Servers. In the Azure portal, open Microsoft Defender for Cloud → Environment settings. Select the subscription, then enable Defender for Servers Plan 1 or Plan 2.
  2. Confirm MDE integration. In Settings and monitoring → Endpoint protection, confirm the status is On. Save.
  3. For Windows Server 2016 / 2012 R2. These versions require the unified agent. In the Monitoring coverage column click Settings → Fix → Unified solution → Enable.
  4. For Linux servers on older subscriptions. If the Linux MDE extension was not automatically deployed, click Fix → Linux machines → Enable to activate it.
  5. On-premises servers. Onboard them as Azure Arc-enabled machines first. Arc registration allows Defender for Cloud to deploy the MDE extension automatically, giving full Plan 2 capability. Direct (non-Arc) onboarding of on-premises servers provides only Plan 1 features.
Verify on Linux Run mdatp health on each Linux server after the extension deploys. The output should show healthy : true and licensed : true. In the Azure portal, confirm the MDE.Linux extension is present on the VM.

2.5 Onboarding via Group Policy (Legacy / Hybrid AD)

Legacy method — consider migrating GPO-based onboarding is supported but is not the recommended path for new deployments. If your environment has Intune, use the EDR policy method in section 2.2 instead. GPO remains appropriate for domain-only environments without modern management.
  1. In the Defender portal, go to Settings → Endpoints → Onboarding. Select OS: Windows 10 and 11, Method: Group Policy. Download the onboarding package ZIP.
  2. Copy the extracted files to a SYSVOL share: \\dc01\SYSVOL\domain\MDE-Onboarding\
  3. Open Group Policy Management Console (gpmc.msc) on the domain controller. Create and link a GPO to the MDE-Ring0 OU.
  4. Edit the GPO: Computer Configuration → Policies → Windows Settings → Scripts (Startup/Shutdown) → Startup. Add the onboarding script.
  5. Devices receive the GPO at next startup or after gpupdate /force. Onboarding completes in the background; device appears in the portal within 30 minutes.

2.6 Verify Onboarding

Defender portal

Go to security.microsoft.com → Assets → Devices. Devices appear within 5–20 minutes of onboarding. Devices managed via Security Settings Management show Managed by: MDE; Intune-enrolled devices show Managed by: Intune.

SENSE service (Windows — run as Administrator)
# Confirm the MDE sensor service is running
Get-Service -Name SENSE | Select-Object Name, Status, StartType
# Expected: Status = Running, StartType = Automatic
KQL — confirm devices are actively sending telemetry
// Devices that have checked in within the last hour
DeviceInfo
| where Timestamp > ago(1h)
| summarize LastSeen = max(Timestamp) by DeviceName, OSPlatform, ManagedBy
| order by LastSeen desc

2.7 Troubleshooting

SymptomLikely CauseFix
Device not in portal after 1 hourSENSE not started or network blockedCheck Get-Service SENSE; verify firewall allows required URLs (section 1.3)
SENSE service stoppedOnboarding script/policy did not completeRe-run script as Administrator; check Event Log → Application
Device shows as InactiveSensor stopped reporting after onboardingCheck internet connectivity and proxy; run MDE Client Analyzer
Security Settings Mgmt: device not receiving policiesEnforcement scope not enabled for platform, or device not in scopeCheck Settings → Endpoints → Enforcement Scope; verify device tag or "All devices" scope
Defender for Cloud: MDE extension not deployedDefender for Servers plan not enabled, or unified solution not activated for legacy OSGo to Environment settings → Monitoring coverage → Fix → enable unified solution
"Tenant already onboarded" errorPackage from a different tenant presentRun offboarding script first, then re-run current tenant's onboarding

Configure Protection

Onboarding gets the sensor installed — but that alone does not give you strong protection. Phase 3 turns on and tunes the actual security controls: cloud protection, attack surface reduction rules, network protection, tamper protection, and device control. The recommended management path is the Defender portal (security.microsoft.com) or the Intune admin center — both surface the same Endpoint Security policy engine. GPO and direct registry are noted where applicable as the legacy alternative.

3.1 Endpoint Security Policy Management

All protection settings in this phase can be managed from two equivalent interfaces that write to the same underlying policy engine:

InterfacePathBest for
Defender portal security.microsoft.com → Endpoints → Configuration Management → Endpoint Security Policies Security team managing policies directly from the SOC workspace
Intune admin center intune.microsoft.com → Endpoint security IT/endpoint management team or organizations with existing Intune workflows

Available policy types in both interfaces:

Security Settings Management Devices managed via Security Settings Management (non-Intune-enrolled) receive Endpoint Security policies directly from the MDE sensor. Intune enrollment is not required — only the MDE sensor needs to be present.

3.2 Cloud Protection (NGAV)

Cloud protection

When a file is about to execute, MDE sends its hash to Microsoft's cloud and receives a verdict in milliseconds — before the file can run. This real-time lookup catches novel malware that signature-based antivirus cannot detect. Without cloud protection enabled, MDE is dramatically less effective.

Configure via an Antivirus endpoint security policy:

  1. Go to security.microsoft.com → Endpoints → Configuration Management → Endpoint Security Policies and click Create new policy.
  2. Platform: Windows 10, Windows 11, and Windows Server. Profile: Microsoft Defender Antivirus. Click Create.
  3. Under Cloud protection, configure:
    Cloud-delivered protection level: High+
    Extended cloud check timeout: 50 seconds
    Submit samples consent: Send safe samples automatically
  4. Under Real-time protection, set Turn on real-time protection to Allowed.
  5. Assign the policy to your Ring 0 Entra ID group and click Save.
Verify cloud protection is active

Run on any onboarded device:

Get-MpComputerStatus | Select-Object `
  RealTimeProtectionEnabled,   # Should be True
  IoavProtectionEnabled,       # Should be True (scans downloaded files and email attachments)
  AntispywareEnabled,          # Should be True
  AntivirusEnabled             # Should be True
Legacy alternative — GPO GPO path: Computer Configuration → Administrative Templates → Windows Components → Microsoft Defender Antivirus → MpEngine. Registry keys under HKLM\SOFTWARE\Policies\Microsoft\Windows Defender: MAPSReporting = 2 (Advanced MAPS), CloudBlockLevel = 4 (Zero Tolerance — equivalent to High+), CloudExtendedTimeout = 50.

3.3 Attack Surface Reduction (ASR) Rules

ASR rules

ASR rules block specific attack techniques — for example, blocking Office documents from launching PowerShell, or preventing scripts from executing code downloaded from the internet. Each rule supports three modes: Audit (log only), Warn (notify user and log), or Block (silently block and log). Always start in Audit mode for 7–14 days to catch false positives before switching to Block.

Configure via an Attack surface reduction endpoint security policy:

  1. Go to Endpoint Security Policies → Create new policy. Platform: Windows 10, Windows 11, and Windows Server. Profile: Attack surface reduction rules.
  2. Set each of the following rules to Audit mode initially:
    — Block credential stealing from the Windows local security authority subsystem (LSASS)
    — Block Office applications from creating executable content
    — Block Office applications from injecting code into other processes
    — Block all Office applications from creating child processes
    — Block JavaScript or VBScript from launching downloaded executable content
    — Block execution of potentially obfuscated scripts
    — Block Win32 API calls from Office macros
    — Block executable content from email client and webmail
    — Block untrusted and unsigned processes that run from USB
    — Block persistence through WMI event subscription
  3. Assign to Ring 0 group. After 7–14 days, review events at Reports → Attack surface reduction and switch confirmed-safe rules to Block.
Audit before blocking Some rules can break legitimate applications — for example, the rule blocking Office from spawning child processes may affect macro-heavy workflows. Review all Audit events before enforcing Block mode.

Read the current rule configuration from a device:

# Returns the rule GUIDs and their corresponding action values
Get-MpPreference | Select-Object -ExpandProperty AttackSurfaceReductionRules_Ids
Get-MpPreference | Select-Object -ExpandProperty AttackSurfaceReductionRules_Actions
# Action values: 0 = Disabled, 1 = Block, 2 = Audit, 6 = Warn
Legacy alternative — PowerShell / GPO Rules can be applied with Add-MpPreference -AttackSurfaceReductionRules_Ids "<GUID>" -AttackSurfaceReductionRules_Actions 2, or via GPO at Computer Configuration → Administrative Templates → Windows Components → Microsoft Defender Exploit Guard → Attack Surface Reduction.

3.4 Network Protection

Network protection

Network protection intercepts outbound connections at the kernel level and blocks destinations known to be malicious — phishing sites, C2 servers, malware distribution points. It also forces HTTPS inspection by blocking QUIC/HTTP3, which attackers use to bypass traditional proxies. Configure in Audit mode first, then switch to Enabled after reviewing events.

Network protection is configured in Intune via the Antivirus policy (Microsoft Defender Antivirus profile) or a Device configuration profile — not in the Attack surface reduction policy:

  1. In Intune, go to Endpoint security → Antivirus, create or edit a Microsoft Defender Antivirus profile, and set Enable network protection to Audit mode.
  2. After 1–2 weeks, review events under Reports → Network protection, then change the setting to Enabled.
  3. Optionally block QUIC to force all traffic through inspectable HTTPS — add a Firewall policy rule blocking UDP/443 outbound.
Verify network protection status on a device
Get-MpPreference | Select-Object EnableNetworkProtection
# 0 = Disabled  |  1 = Enabled  |  2 = AuditMode

3.5 Tamper Protection

Tamper protection

Tamper protection locks Defender's settings so they can only be changed through the Microsoft cloud portal — not through registry edits, local PowerShell, or third-party software. Even an attacker with SYSTEM privileges cannot disable Defender when tamper protection is active.

Enable from the Defender portal (tamper protection requires the cloud policy — it cannot be fully enforced via local PowerShell or GPO alone):

  1. Go to security.microsoft.com → Settings → Endpoints → Advanced features.
  2. Find Tamper protection and toggle it On.
  3. Click Save preferences.
  4. Verify on a device: Get-MpComputerStatus | Select-Object IsTamperProtected — should return True.
Need to make temporary changes? Use Troubleshooting Mode If you need to temporarily bypass tamper protection on a device (for example, to test configuration changes), use Troubleshooting Mode in the Defender portal rather than disabling tamper protection. Troubleshooting Mode limits the bypass window and logs all changes. Go to security.microsoft.com → Assets → Devices → click the device → Turn on troubleshooting mode.

3.6 Device Control — Managing Removable Media

Device control

Device control defines what removable storage devices (USB drives, external drives, phones in file transfer mode) can do on company devices. You can block all removable storage, allow read-only access, or permit only approved devices — preventing both data exfiltration and malware introduction via USB.

Deploy device control via OMA-URI in an Intune configuration profile, or through the Attack surface reduction policy. The policy requires two XML files — one defining device groups, one defining access rules:

<!-- DeviceControlGroups.xml — Define which devices to target -->
<Groups>
  <Group Id="{6b2e2ec9-8b73-4f34-a4a8-aeb7b3b0c95d}" Type="Device">
    <Name>All Removable Storage</Name>
    <MatchType>MatchAny</MatchType>
    <DescriptorIdList>
      <PrimaryId>RemovableMediaDevices</PrimaryId>
    </DescriptorIdList>
  </Group>
</Groups>
<!-- DeviceControlPolicyRules.xml — Define what to DO with matched devices -->
<PolicyRules>
  <PolicyRule Id="{c544a991-5786-4402-949e-a032cb790d0e}">
    <Name>Block All Removable Storage</Name>
    <IncludedIdList>
      <GroupId>{6b2e2ec9-8b73-4f34-a4a8-aeb7b3b0c95d}</GroupId>
    </IncludedIdList>
    <ExcludedIdList/>
    <Entry Id="{1ecfde36-1a49-4d11-9ece-e8ee6e4e5b56}">
      <Type>Deny</Type>
      <AccessMask>63</AccessMask>
      <Options>0</Options>
    </Entry>
  </PolicyRule>
</PolicyRules>
AccessMask values 1 = Disk read, 2 = Disk write, 4 = Disk execute, 8 = File system read, 16 = File system write, 32 = File system execute, 64 = Print. Add values to combine permissions. 63 = block all disk and file system operations (does not include print). To allow read-only access, use AccessMask 9 (disk read + file system read).

Investigate & Respond

Protection prevents most attacks, but no system blocks everything. Phase 4 teaches you how to investigate an incident when one occurs — how to read an alert, how to use Advanced Hunting to trace what happened, and how to contain and remediate a threat using Live Response and isolation. This phase also includes a full ransomware investigation walkthrough.

4.1 Understanding Alerts — How to Read What MDE Is Telling You

What is an alert?

An alert is MDE's way of telling you it detected suspicious activity. Each alert has a severity (Informational, Low, Medium, High), a MITRE ATT&CK technique mapping (so you know what the attacker was trying to do), a device name, a timestamp, and an evidence tree showing exactly which process did what. Alerts are grouped into incidents when they appear related — multiple alerts from the same attack will be in a single incident so you can see the full picture.

Use this KQL query in Advanced Hunting to get a summary of recent alerts on your environment:

// Summary of all alerts in the past 7 days, grouped by severity
// Run this in: security.microsoft.com → Hunting → Advanced Hunting
AlertInfo
| where Timestamp > ago(7d)              // Look at the last 7 days
| summarize AlertCount = count()          // Count the number of alerts
    by Severity,                          // Group by severity level (High, Medium, Low)
       Category,                          // Group by attack category (e.g. Malware, Ransomware)
       DetectionSource                    // Which engine generated the alert
| order by case(                          // Sort so High severity appears at top
    Severity == "High", 1,
    Severity == "Medium", 2,
    Severity == "Low", 3,
    4), AlertCount desc

4.2 Advanced Hunting — Searching for Threats with KQL

What is Advanced Hunting?

Advanced Hunting is a search interface in the Defender portal where you can query up to 30 days of raw security data using KQL. Every file creation, process launch, network connection, registry change, and login attempt on every onboarded device is stored here. This lets you answer questions like "has any device on our network ever connected to this suspicious IP address?" or "which computers ran this malicious file in the last month?"

Here are the most important hunting queries, with each line explained:

// HUNT 1: Find all devices that ran a specific suspicious file hash
// Replace the SHA256 hash below with the hash of the file you are investigating
DeviceFileEvents
| where Timestamp > ago(30d)              // Search the last 30 days of data
| where SHA256 == "REPLACE_WITH_FILE_HASH_HERE"  // Match this specific file
| project                                 // Show only these columns (cleaner output)
    Timestamp,                            // When the event happened
    DeviceName,                           // Which computer
    FileName,                             // What the file was named
    FolderPath,                           // Where it was located
    InitiatingProcessFileName,            // What process created or accessed the file
    InitiatingProcessCommandLine          // The full command line that ran it
// HUNT 2: Find PowerShell commands that look suspicious (encoded or download commands)
// Attackers often use -EncodedCommand or download cradles to hide malicious scripts
DeviceProcessEvents
| where Timestamp > ago(7d)
| where FileName in~ ("powershell.exe", "pwsh.exe")  // Match PowerShell (case-insensitive)
| where ProcessCommandLine has_any (                  // Look for these suspicious patterns
    "-EncodedCommand",    // Base64-encoded command — common obfuscation technique
    "-enc",               // Short form of -EncodedCommand
    "IEX",                // Invoke-Expression — runs a string as code
    "Invoke-Expression",  // Same as above, spelled out
    "DownloadString",     // Downloads content from the internet and runs it
    "WebClient"           // Creates a web connection — often used to download malware
  )
| project Timestamp, DeviceName, ProcessCommandLine, InitiatingProcessFileName
| order by Timestamp desc
// HUNT 3: Network connections to unusual ports or IPs — signs of C2 communication
// Command-and-control (C2) traffic is how malware calls home to the attacker
DeviceNetworkEvents
| where Timestamp > ago(24h)
| where ActionType == "ConnectionSuccess"             // Only successful connections
| where RemotePort !in (80, 443, 53, 25, 587, 8080)  // Filter out common legitimate ports
| where RemoteIPType != "Private"                     // Ignore internal network traffic
| summarize                                           // Aggregate to find patterns
    ConnectionCount = count(),
    Devices = dcount(DeviceName)                      // How many unique devices connected
    by RemoteIP, RemotePort, RemoteUrl
| where ConnectionCount > 5                           // Focus on repeated connections
| order by ConnectionCount desc

4.3 Device Isolation — Containing a Compromised Machine

What is device isolation?

When you confirm a device is compromised, the first response action is isolation: cutting the device off from all network communication so the attacker cannot issue new commands, exfiltrate data, or spread to other machines. An isolated device retains its connection to the MDE cloud portal only — so you can still investigate it and send Live Response commands — but it is completely cut off from the corporate network, the internet, and other devices.

Isolate a device via the Defender portal OR via the REST API (useful for automation):

# Isolate a device using the Microsoft Defender for Endpoint REST API
# Use this in a SOAR playbook or when you need to isolate many devices at once

# Step 1: Get an authentication token from Microsoft Entra ID
# Replace the values below with your actual tenant and app registration details
$TenantId  = "YOUR-TENANT-ID"         # Your Microsoft 365 tenant ID (GUID)
$ClientId  = "YOUR-APP-CLIENT-ID"     # App registration client ID from Entra ID
$ClientSecret = "YOUR-CLIENT-SECRET"  # Client secret from the app registration

# Request an OAuth2 token from Microsoft identity platform
$TokenResponse = Invoke-RestMethod `
  -Method POST `
  -Uri "https://login.microsoftonline.com/$TenantId/oauth2/v2.0/token" `
  -Body @{
    client_id     = $ClientId
    client_secret = $ClientSecret
    scope         = "https://api.securitycenter.microsoft.com/.default"
    grant_type    = "client_credentials"  # Machine-to-machine auth (no user login)
  }

$AccessToken = $TokenResponse.access_token  # Extract the bearer token

# Step 2: Send the isolation request for the target device
$DeviceId = "DEVICE_ID_FROM_MDE_PORTAL"  # Find this in: Assets → Devices → click device

Invoke-RestMethod `
  -Method POST `
  -Uri "https://api.securitycenter.microsoft.com/api/machines/$DeviceId/isolate" `
  -Headers @{ Authorization = "Bearer $AccessToken"; "Content-Type" = "application/json" } `
  -Body (@{
    Comment       = "Isolating suspected ransomware infection - incident 1234"  # Required field
    IsolationType = "Full"  # Full = all traffic blocked except MDE portal
                            # Selective = allows Outlook and Microsoft Teams through
  } | ConvertTo-Json)

Write-Host "Isolation request sent. Device will appear as Isolated in the portal within 2 minutes."

4.4 Ransomware Investigation Walkthrough

What does a ransomware attack look like in MDE?

Ransomware typically follows a predictable pattern: initial access (phishing or exploit), privilege escalation, credential theft, lateral movement to spread across the network, and finally the encryption payload. MDE detects activity at each stage. The queries below let you reconstruct the full attack timeline from the telemetry MDE collected.

// RANSOMWARE HUNT: Find mass file encryption activity
// Ransomware renames or overwrites thousands of files very quickly
// This query looks for processes that modified an unusually high number of files
DeviceFileEvents
| where Timestamp > ago(1h)               // Focus on the last hour (active incident)
| where ActionType in ("FileCreated", "FileModified", "FileRenamed")
| summarize
    FilesModified = count(),              // Total files touched
    UniqueExtensions = dcount(FileName),  // How many different file types
    SampleFiles = make_set(FileName, 5)   // Show up to 5 example file names
    by DeviceName, InitiatingProcessFileName, InitiatingProcessId
| where FilesModified > 100              // Flag processes that touched 100+ files
| order by FilesModified desc
// RANSOMWARE HUNT: Look for shadow copy deletion (a ransomware signature)
// Ransomware deletes backup copies (shadow copies) to prevent recovery
// vssadmin.exe delete shadows is the most common command used
DeviceProcessEvents
| where Timestamp > ago(24h)
| where ProcessCommandLine has_any (
    "vssadmin delete shadows",    // Most common shadow copy deletion command
    "wmic shadowcopy delete",     // Alternative WMI-based method
    "bcdedit /set recoveryenabled no",  // Disables Windows Recovery
    "wbadmin delete catalog"      // Deletes Windows backup catalog
  )
| project Timestamp, DeviceName, ProcessCommandLine, AccountName, InitiatingProcessFileName
| order by Timestamp desc

4.5 Live Response — Remote Forensics and Remediation

What is Live Response?

Live Response gives you a command-line session on any onboarded device, even if the device is isolated and the user is not logged in. You can browse files, download forensic evidence, run scripts, kill processes, and remove malware — all without physically touching the machine. This is essential for incident response when the affected device is in a remote office or a datacenter.

To start a Live Response session: go to security.microsoft.com → Assets → Devices → click the device → Initiate Live Response Session. Then use these commands:

# Common Live Response commands
# These are run inside the Live Response terminal in the Defender portal

# List running processes — look for suspicious process names or unsigned binaries
processes

# List files in a directory
dir C:\Users\Public\

# Download a suspicious file for analysis (saves to your portal Files library)
getfile "C:\Users\Public\suspicious.exe"

# Run a script from your portal library on the remote device
run ForensicCollect.ps1

# Remove a malicious file from the device (use -auto to skip confirmation)
remediate file "C:\ProgramData\malware.exe" -auto

Coexistence & Advanced Topics

Most organisations already have an antivirus product installed before deploying MDE. This phase explains how to handle that transition safely — and covers advanced topics including RBAC setup, automated investigation, and continuous vulnerability management.

5.1 Running MDE Alongside Another Antivirus

Why this matters

When a third-party antivirus (like CrowdStrike, Symantec, or Sophos) is installed, Windows automatically puts Microsoft Defender Antivirus into Passive Mode. In passive mode, Defender does not scan files or block threats — but it still collects EDR telemetry. This is intentional: you get the investigation data without the two antivirus engines conflicting. The danger is that some teams disable Defender entirely rather than leaving it in passive mode, which eliminates the EDR visibility entirely.

Defender ModeReal-time ScanningEDR TelemetryWhen to Use
ActiveYesYesMDE is the only AV — no third-party AV installed
PassiveNoYesThird-party AV installed — Defender provides EDR only
EDR Block ModeNo (reactive only)YesThird-party AV installed but you still want Defender to block detected threats
DisabledNoNoNever — this removes all protection and visibility
Never disable Microsoft Defender entirely Setting Defender to Disabled mode removes EDR telemetry completely. Even if CrowdStrike handles all the blocking, you lose the ability to investigate incidents in the Defender portal. Always leave Defender in Passive or EDR Block mode when a third-party AV is present.
# Check current Microsoft Defender operating mode
Get-MpComputerStatus | Select-Object AMRunningMode
# Possible values:
#   Normal         = Active mode (Defender is the primary AV)
#   Passive         = Passive mode (third-party AV detected)
#   EDR Block       = EDR Block mode (enabled manually)
#   SxS Passive     = Side-by-side passive (limited periodic scanning mode)

# Enable EDR Block mode when a third-party AV is installed
# This allows Defender to block threats it detects even in passive mode
# Note: third-party AV must still be the primary real-time scanner
Set-MpPreference -ForceDefenderPassiveMode $false  # Must be false for EDR Block to work
# Then enable EDR Block via registry:
Set-ItemProperty `
  -Path "HKLM:\SOFTWARE\Policies\Microsoft\Windows Advanced Threat Protection" `
  -Name "ForceDefenderPassiveMode" `
  -Value 0  # 0 = allow EDR Block mode; 1 = force passive (no blocking)

5.2 Role-Based Access Control — Who Can Do What in the Portal

What is RBAC in MDE?

RBAC controls which analysts can see which alerts and take which actions. Without RBAC configured, every person with portal access can see everything and take any action — including isolating devices or deleting investigations. Proper RBAC means a Tier 1 analyst can view and triage alerts, a Tier 2 analyst can run Live Response and isolate devices, and only security administrators can change global settings.

RoleView AlertsManage AlertsLive ResponseIsolate DevicesChange Settings
Tier 1 Analyst (Read-only)YesNoNoNoNo
Tier 2 AnalystYesYesYes (basic)YesNo
Tier 3 / Threat HunterYesYesYes (advanced)YesNo
Security AdministratorYesYesYes (advanced)YesYes

Create custom roles in the portal: go to Settings → Endpoints → Roles → Add item. Assign roles to Entra ID security groups for easy management.

5.3 Automated Investigation & Remediation (AIR)

What is AIR?

AIR is MDE's built-in automation engine. When an alert fires, AIR automatically investigates: it collects process trees, file data, network connections, and registry changes, then uses AI to determine if the activity is malicious. If it is confident, it automatically removes the threat (deletes files, kills processes, reverses registry changes). This can resolve incidents in minutes that would otherwise take an analyst hours to investigate. Requires MDE Plan 2.

Automation LevelWhat it DoesWhen to Use
No automated responseInvestigations run; no remediation actions takenInitial testing phase
Semi — require approval for any remediationProposes all remediation actions; analyst must approve eachDuring transition; cautious environments
Semi — require approval for core folders remediationAuto-remediates outside core OS folders; approval required for system/program files directoriesOrganisations with mature alert triage
Semi — require approval for non-temp folders remediationAuto-remediates files in temp folders; approval required for all other locationsMost enterprises (recommended starting point)
Full — remediate threats automaticallyAutomatically remediates all confirmed threats without human approvalMature SOCs with high confidence in MDE verdicts

Set the automation level in the portal: Settings → Endpoints → Device groups → Edit device group → Automation level. Start with "Semi — require approval for all remediations" and move to Full automation after you have observed AIR's decisions for 4–8 weeks.

5.4 Threat & Vulnerability Management (TVM)

What is TVM?

TVM continuously scans every onboarded device for missing patches, weak configurations, and known vulnerable software. Unlike traditional vulnerability scanners that run weekly scans, TVM uses the MDE sensor (which is already on every device) to provide real-time visibility. It prioritises vulnerabilities by combining the CVSS score with real-world data about whether attackers are actively exploiting the vulnerability — so you focus on what actually matters.

// Find the top 10 most critical vulnerabilities across your estate
// Prioritised by exploit availability and device exposure
DeviceTvmSoftwareVulnerabilities
| where VulnerabilitySeverityLevel == "Critical"        // Only Critical CVEs
| summarize
    ExposedDevices = dcount(DeviceId),                   // How many devices are affected
    DeviceList     = make_set(DeviceName, 5)             // Sample affected device names
    by CveId,                                            // Group by CVE identifier
       SoftwareName,                                     // What software has the vulnerability
       SoftwareVersion,                                  // Specific version
       RecommendedSecurityUpdate                         // What patch fixes it
| order by ExposedDevices desc                           // Prioritise by most affected devices
| take 10                                               // Show top 10

Deployment Checklist

Use this checklist to track your deployment progress. Work through each phase in order — each item corresponds to a section in this guide.

PhaseItemSection
Phase 1Confirmed MDE Plan 2 license is assigned to the tenant1.1
Phase 1Verified all target OS versions are supported1.2
Phase 1All required URLs are whitelisted in firewall/proxy1.3
Phase 1MDE Client Analyzer run on pilot machine — all URLs reachable1.3
Phase 1Deployment rings defined and AD OUs created1.4
Phase 2Onboarding package downloaded from portal2.2
Phase 2GPO created and linked to Ring 0 OU2.3
Phase 2SENSE service confirmed running on Ring 0 devices2.4
Phase 2Ring 0 devices visible in Defender portal2.4
Phase 2GPO expanded to Ring 1 and Ring 22.3
Phase 3Cloud protection (MAPS) enabled — CloudBlockLevel 63.1
Phase 3ASR rules deployed in Audit mode3.2
Phase 3ASR audit findings reviewed; rules promoted to Block3.2
Phase 3Network protection enabled in Audit, then Block3.3
Phase 3QUIC blocking firewall rule applied3.3
Phase 3Tamper protection enabled from portal3.4
Phase 3Device control policies deployed and tested3.5
Phase 4Advanced Hunting baseline queries saved4.2
Phase 4Incident response runbook tested (tabletop exercise)4.4
Phase 5AV coexistence mode verified (Passive or EDR Block if needed)5.1
Phase 5RBAC roles created and analyst accounts assigned5.2
Phase 5AIR automation level configured5.3
Phase 5TVM baseline exposure score reviewed5.4
You have completed the MDE deployment roadmap If every item above is checked, your organisation has a fully operational Microsoft Defender for Endpoint deployment — from licensing through to advanced hunting, incident response, and vulnerability management.