That was supposed to be an option. (Sorta)

The ending was supposed to reveal that like, the Reapers were a billion year long plan to prevent some oncoming apocalypse or something. And you had the choice to destroy them or let them destroy you.

Then again, this is hearsay about cut content from a video game.

@Khan: If I could help write Mass Effect 4 I'd be the happiest man alive, Mass Effect has a bit more meaning to me than I'm willing to divulge.