Can't remember were I read, likely the Mass Effect 3 Thread on SB.Com, but the Alliance took the SR-2 apart, to see what made it tick (in all likely hood, fully upgraded SR-2, is cannon), plus getting there hands on that A.I., which isn't an Homicidal Manic, would be a bonus.
Oh then they put it back together. But this is not an Cerberus Frigate anymore, it's Alliance....so no more Leather seats, Jokers gonna be pissed.