But if Indoctrination Theory is cannon then there wouldn't be a destroy ending. Because Shepard never would have destroyed the Reapers, and it would have been all in his head. Which means that the Alliance fleet would be destroyed as their only hope was Shepard activating the Crucible which can't happen under Indoctrination Theory.
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Unless of course Indoctrination Theory is true and then they were firing on Shepard because they knew he was indoctrinated and wouldn't be able to save them...