This is by far my biggest beef with the game, even beating out God Child. It, literally, has no explanation. At least God Child is based on some (albeit stupid and out of the blue) premise in the series, however circular it may be.
You really want to know why the normandy is running off? You sure? Because you can't go back.
http://www.youtube.com/watch?v=QjWlb-99ZHs&ob=av3n
This is the worst ending you can get. For this, the blast provided from the destroy option, destroys everything including earth and all the space junk (19:28). Normandy is speeding off to evade that explosion.
They simply applied the scene of the normandy running off, to every ending. And as you know, the blast isn't that damaging in all the endings.
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