Restore from external

Okay, so my desktop computer won't boot. When I turn it on it displays the welcome splash screen and then goes black. A message will then display that says CMD failed to start and then it will shut down. It does the same thing in safe mode as well.
(I clicked on a questionable file and aparently it was the bad kind   ) If there is anyway to fix that that would be great.

My question is. I have already set up the HD from the desktop as an external to my laptop so I could get files off it.
Is there any way to do system restore on the hard drive when it is set as an external? Because I did this last night and I think if I restore the drive it will fix it.

Any help is appreciated.

Thanks.