User blog comment:JakePT/The New Normandy/@comment-3053284-20110425103528/@comment-1691295-20110425105038

I don't think he is. By the sounds of it Shepard's basically been arrested (or turned himself in) for Arrival, and the Alliance has effectively stolen the ship and torn it apart.

It sounds like that when the Reaper attack occurs Shepard escapes to where the Normandy is being held and basically steals the new Alliance version back.