How to Use Windows Defender Offline Scan to Remove Hidden Malware

4 min read

Windows Defender Offline Scan runs before Windows loads, catching rootkits and malware that hide from normal scans. How to start it, what it does, and how to read the results.

Some malware hides from antivirus tools by loading itself before Windows — or by hooking into running processes. The only way to detect and remove it is to scan before Windows starts. That's what Windows Defender Offline Scan does.


What It Does Differently

A regular Windows Defender scan runs while Windows is active. Sophisticated malware can:

  • Intercept file reads to hide itself
  • Disable antivirus processes
  • Reload after being "removed"

The Offline Scan boots into a minimal environment outside of Windows, then scans your drive. Malware can't hide or interfere.


When to Use It

  • Normal scans detect threats but can't remove them
  • PC is behaving strangely but regular scan shows nothing
  • You suspect a rootkit
  • After visiting a compromised website
  • Before selling or repurposing a PC

Start the Offline Scan

Method 1: Windows Security

Win + SWindows SecurityVirus & threat protectionScan options → select Microsoft Defender Antivirus (offline scan)Scan now

Windows will warn you that the PC will restart. Save and close everything → click Scan.

Method 2: PowerShell

Start-MpWDOScan

The PC restarts automatically and begins scanning.


What Happens During the Scan

  1. PC restarts into the Windows PE (pre-installation) environment
  2. Defender loads with the latest definitions
  3. Full system scan runs — takes 10–20 minutes
  4. PC restarts back into Windows normally

You'll see a blue progress screen with a percentage counter. Don't interrupt it.


View the Results

After the PC restarts, open Windows SecurityVirus & threat protectionProtection history

Look for recent entries from the offline scan. Threats found will show as Quarantined or Removed.

Via PowerShell:

Get-MpThreatDetection |
  Where-Object {$_.ActionSuccess -eq $true} |
  Select-Object DetectionID, ThreatName, ActionSuccess, Resources |
  Sort-Object -Descending

Update Definitions Before Scanning

Outdated definitions miss newer threats. Update first:

Update-MpSignature

Or: Windows SecurityVirus & threat protectionProtection updatesCheck for updates


If Threats Were Found But Not Removed

Some malware resists removal even from offline scan. Next steps:

  1. Note the malware name from Protection History
  2. Search Microsoft's Malware Encyclopedia for specific removal instructions
  3. Run the scan again — sometimes requires two passes
  4. Consider using Malwarebytes Free as a second opinion scanner
  5. Last resort: reset Windows

Combine With Full Scan

For thorough cleaning, run both:

# First, offline scan (requires restart)
Start-MpWDOScan

# After restart, run a full scan
Start-MpScan -ScanType FullScan


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Summary

Windows SecurityScan optionsMicrosoft Defender Antivirus (offline scan)Scan now. Update definitions first. The scan takes 15–20 minutes and requires a restart. Check Protection history for results afterward. Use this when regular scans aren't working or you suspect a rootkit.

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