The Humans get sick of the Cybertronians and don't want them to bring their war to Earth, and tell them to gtfo. This happens as some sort of meeting or whatever, between OP, Megs, and some Cybertronian tech or smth providing a hologram or visual of said human telling both factions to leave. The human cities surrounding the area have all been evacuated, with absolutely NOBODY there, 'to keep the Cybertronians secret', they thought. (Or something, as long as all/most humans are away from the area)

But when both the Autobots and Decepticons refuse, for whatever reason, the humans are like 'so be it', and cut of contact before privately issuing an order to some military ppl idk.

And then the humans pretty much jump/ambush everyone, from the air, herding them all onto the Nemesis or whatever. Except for Optimus and Megatron, who realize they're all being chasing into one spot, and try to stop everyone, but it's too late.

The humans fragging nuke the Nemisis.

And Optimus and Megatron are the only ones who survive, albeit too injuried and weak to do anything but pass out as the humans' "clean up crew" come in and drag them off to containment.

Preferably, every 'bot and 'con on Earth were the total remaining Cybertronians.

So, in the end, Optimus and Megatron, the ones who started this all, who were the leaders of their factions, who had been at war with eachother for so long are the only ones left. The only two who survived.