Theory #1: Nemesis Prime
It's been years after Optimus Prime left Earth to find his creators. Ever since, Rodimus Prime, Optimus Prime's son, is leading the Autobots.
However, Optimus Prime quickly finds the Creators. They kidnap Optimus Prime and create a clone of Optimus Prime to destroy Earth.
Meanwhile, back on Earth, Rodimus Prime and the Autobots battle Galvatron and a new group of Decepticons when Nemesis Prime, under the guise of Optimus Prime, joins the battle and saves Rodimus Prime.
Rodimus Prime and the other Autobots rejoice that "Optimus Prime" has returned. However, the humans start to get suspicious.
Things reach a boiling point when Nemesis Prime reveals himself and kills an Autobot. Nemesis Prime then joins the Decepticons, pushing Galvatron out of leadership.
Rodimus, who is appalled by the actions of Nemesis Prime, forms an uneasy alliance with Galvatron, in which the two and the new alliance of Autobots and Decepticons take down Nemesis Prime.