Why does Windows Vista have two programs to remove viruses:
Windows Defender and Microsoft Windows Malicious Software Removal Tool (MRT)
Windows Defender runs in the background as real-time protection, looking for suspicious activities on your computer in order to prevent a break-out.
You can use the Malicious Software Removal Tool (mrt.exe) to scan for malicous software which has already infected your computer.
Windows Defender is an "active" running program. It is designed to detect and block entry of malicious programs before you have a security issue.
Malicious Software Removal Tool is designed to run after the fact. If your system is breached, you'll run this instead.