It won't get nearly as stupid as Condemned 2's ending. And I take some comfort in that.
They could do it deus ex machina style, have some last minute weapon, ally, or weakness show up. Computer virus, space-god, control ships. Or maybe, just maybe, it'll be a fleet battle cinematic after beating up the Reaper's leader (gotta have a boss fight).
Or they'll all jump into humanoid robot skeletons at the last second and die off to assault rifles. Again. That's another possibility.