TIMELINE THEORY: Friendship In Disguise, but Cutie-Remarked.
 
Without Dash’s rainboom, the Mane 6 never stood up to Megatron and Chrysalis. Without the Mane 6, Prime’s Matrix of Leadership wasn’t enough to stop Megatron (maybe he got his servos on the Elements, causing him to be more powerful than the Matrix). Soon the Autobots were defeated, and most are either imprisoned or executed by the Decepticons. The Decepticons then went to terrorize the ponies with their advanced weaponry and defeated Celestia. Soon, the ponies had to bow down to Megatron while living a living Tartarus.