It's too early to say until the scan is done.
I don't know what A PC Tools anti-virus is. It's not one of the recognised AVs.
You say don't bother with links, and also you can't transfer application set up files to this computer from a flash drive, and if you can do neither then then the outlook isn't good.
But assuming you are using Windows, (which one), Safe Mode may work, or Safe Mode with Networking. Many viruses and malware don't get a hold in safe mode.
Mark
I cannot navigate via the desktop icons on one of my laptops. An Open with window appears instead of automatically opening the selected program. I CANNOT access the internet, so suggesting a link on line to fix it is not going to work as suggested in other forum questions similar to mine. Trying to use an good computer to download to a flash drive so I can put fixes on the bad computer are not working. I am so far successfully running A PC Tools antivirus that has picked up a
Trojan.Maljava virus that maybe my problem. There is an hour to go on the scan, so I will not know if fixing it will solve this issue. So, I am asking this now in case it does not. any suggestions?

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic