It's been a bit more than a day since I posted the ship, so I'm going to end the "contest" here. Many of you either had really good ideas, really good ideas that are (to my knowledge) impossible (unless you are LazyWizard, maybe?)
but I still got a ton of free good ideasAnyway:
The best alternative I can come up with is that it's some sort of superweapon (EMP of dooom!)
Wyvern wins, because of his suspicion that it's related to some sort of energy emitter system. It's going to be that, or if it turns out unsatisfactory, or I get coding help, I'm going to try for some sort of novel defensive system instead. (Kaitol touched upon some of those ideas, specifically the reflective shield, but I figured it's mechanically impossible too, so)
Wyvern, if you want that Dota 2 invite, send me your steam ID or mail address on PM. Woo! EDIT: Wyvern doesn't want the invite. You know what, I'll give away all three, all my peeps already play the game anyway. Three first to PM me get invites.