Not sure if anyone else has this issue on this quest but the optional part is to get the leader of the Brotherhood Elder McNamara ousted so that a new leader is put forth.

If you choose the dialogue associated with a high science skill (70 I believe), you're able to partition terminals which the virus jumps to. After you partition 3 terminals, the quest cannot advance any further. No other terminals will have the virus jump to it, and you're not given a solution to the quest in any way.

I think I can complete the quest which I'm going to try now but can't complete it the way I wanted by changing the leader of the brotherhood of steel, or so I think, unless there's another way?