When Megatron, Emperor of Destruction, heads to Equestria to find Mini-Cons, he discovers that the Crystal Empire is more peaceful than a regular empire. He plans to rebuild the Crystal Empire into a faction of evil and wants everyone to serve under him. The Mane 6 must stop Megatron and his subordinate, Starscream before Megatron can launch an attack on Canterlot and take over Equestria, forever while Rarity must stop Sweetie Belle from adopting her new brother...
Timelines:
Transformers: Set in the TF Armada universe.
MLP: Set after Starlight Glimmer joins the Mane 6.