So I was thinking about whether this should be a sequel, prequel, midquel. And I figured, why not all at the same time? Go all David Lynch on our ass and thereby salvage the original series.
So destruction is the canonical ending, but Shepard as he blows up the catalyst, gets hit by the space magic and gleans the future, while simultaneously becoming a transcendental being. Turns out the Reapers were actually made to keep the Leviathans in check. Unbridled, the take over the world and destroy all of life, not just the sentient ones. So Shepard, being transcendental is able to project himself into the past, without being able to actually physically influence it. Turns out he was actually The Illusive Man all along, or at least the one indoctrinating TIM, trying to push Shepard into choosing control. Only of course he fails, so now you are a new person, who has to find a remaing catalyst piece and sacrifice yourself, so you can astrally project yourself and try to indoctrinate Anderson into stopping Shepard from killing TIM.
No?
Please?
Oh all right.