Well I got the problem fixed. But you say that yet it was an .exe format (not saying that's automatically a virus). I checked the .exe and it wanted to install a bunch of programs. So then I cancel it and guess what? The programs are there anyway. I run a virus scan and I have at least 50 malware and trojans. I figure now it was most likely a guy who said he made it then gave me a bunch of viruses. I only trusted it because mods like Berlin were in an .exe. Thanks for the input though.
The Bieberfelde Mod as it turns out has many viruses in it. Now I have removed the malware and trojans, but no games (including EM4) will launch. I try to run EM4, get a black screen, and then it crashes.