How exactly am I supposed to isolate the virus?

You have to find the Virus on 3 terminals in 60 seconds to wipe it from the system. Quickly enter each terminal and choose the only option you can. Then, if the text that shows up seems like a random string of letters and numbers, proceed to the next terminal. If you get a taunting message on the second screen, choose the option to isolate the virus. The infected terminals are almost always in a row or close together in a group. The virus usually has one per section(such as 1 in the middle). If you don't get all 3 terminals in the time limit, you have to speak with Ibsen again.

Sometimes saving right before Ibsen says, "ok, the virus just jumped", which should be right before you begin, save right before this. I just kept loading my game and looking for the terminals. After about five minutes I got the hang of it, and completed the side quest.

The virus in question was loaded onto the Bunker network when a scribe found a holodisc in the wilderness and like an idiot inserted it into an unprotected computer in the Bunker, thus infecting it and so the network.

How you deal with it is really simple - this is a timed quest by the way - and all that you need to do is, as fast as you can, find the virus on three terminals in the Bunker within 60 seconds and "isolate it" on them.

When you access a terminal there is only one option you can choose - if you get a random text go to the next one, and once you get a taunting message you have found a virus infected terminal, and you should use the isolate command.

You need to do this in three random terminals, though in my experience they are usually pretty close together. You can use a dose of turbo if you find you are not going fast enough and time out - if that happens you just need to speak to the scribe again to reset the quest and timer.