CPU virus question

If he can get in as Administrator and get to security updates and use control panel and run Malwarebytes it's not a very good rootkit. Rootkits replace the kernel and you are no longer even running Windows, you are running malware that runs Windows for you, meanwhile it can do whatever it wants with your computer. Keep track of your every keypress, decode encrypted transactions, read any file and hide some from you, turn on your webcam and microphones, anything.
I like Malwarebytes. I just happen to carry SAS around on a thumb drive with me.