For about several days to weeks the autobots on earth successfully take down business of corrupted autobots and other straggling decepticons in other cities. Ultra Magnus left in stasis for another several weeks and Sentinel becomes the new supreme commander, until Ultra Magnus awakes and he announces who the leader should really be.
He then sends Strika and her very own team to free Megatron and all of the Decepticons to find the All Spark fragments that were still all over earth for he can absorb its power. He responds to the activation of the allspark turning into a new powerful source to rebuild their army. Meanwhile on the decepticon's new homeworld, The Fallen has finally awoken for the first time in Centuries. In season 4, Megatron and all of the other Decepticons are in prison on Cybertron and the Autobots have returned to Cybertron.