What OS are you running? and if it's Windows 7 or above isn't Microsoft Security Essentials genuine?

If a system is beyond repair only the hard drive needs changing or wiping at worst to have the computer ready for work again. No need to bin it.

Root kits, I know nothing.

I used to scan my systems with a command in a Terminal and you have reminded me I haven't done it for a while and so it needs doing.

https://help.ubuntu.com/community/RKhunter