Last night I had a Windows 2003 web server become compromised. It appears the attacker deleted the boot.ini / NTLDR files to prevent the system from starting up. The problem was a little tricky to troubleshoot, but with the right tools I was able to resolve the issue relatively quickly. Incase anyone runs into the same problems below are a good set of steps to troubleshoot.
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows Server 2003, Standard" /fastdetect
I believe I dodged a bullet here. The web server was still had all the site files, and all the data. The individual beyond this could have easy do more damage then they did.