[spoiler]An awacs, but autopilot is something you can turn off dude, pilots don't like to use it, and never use it in a combat scenario like this.[/spoiler] The virus was only in the one aircraft, having no path to the other aircraft. The aircraft's computer was not advanced enough to interface and network with others. Whoever he was expecting to fight with this, these were not those guys.

(Unfortunately, the virus had moved from the comms channels of the other ships, to the headset of the pilots, to the wings) [spoiler]it can't be off. It can only not currently be used[/spoiler]

[spoiler]again, not as high tech as you think. And while the auto pilot is disabled it has no control over the aircraft, this is to prevent it from killing the pilot if he's trying to do maneuvers and evade, even when it's on, the pilot's controls overwrite the system.[/spoiler] The virus was isolated.