I had this thought earlier that resulted in a longish blog post; to try and keep it a bit shorter:
Bernhard Strauss seemed to be up to something with the ten battleroids--and in fact seemed to have plans for the entire ship--but nothing came of it (due to the invasion). Even knowing how powerful battleroids are, though, ten feels like a very insufficient number to take over a Deimos-sized vessel (and even if these guys weren't part of the same generation that got out of control, there's bound to be some sort of anti-battleroid safeguards in place).
However, Strauss knows how damaging a Rampant AI can be to your systems, and it just so happens that he's trying to make one of his own constructs go Rampant FOR SCIENCE. He convinces someone to take Durandal to the Marathon to serve as Operations.
Strauss's buddies (MIDA?) have already hidden ammo caches all over the ship; he just has to wait for Durandal to finally snap and take down the systems. In the ensuing chaos, Strauss and co. go around shanking higher-ups until there's no more higher-ups left to shank. They neutralize Durandal--and his siblings, if need be--and the Marathon is theirs.
...of course, this plan assumes a lot of things: that Strauss could regain control over Durandal so easily, that Durandal wouldn't murder him in stasis or with a MADD, that Durandal wouldn't hail a bunch of hostile aliens and partner up with one of the battleroids, etc. etc. Sociopaths tend not to think that far ahead.
What say? Really hope that no one here already thought of this.