So, the AU is called Apocalypse Protocol. It's set in the bad future of the Kraang with things significantly changed, like the guys' past and their relationships with other characters.
It also puts in a few OCs, some that were intended for TMNT, like Catarina and Scotty, and some that ended up being added thanks to the Misa-dventures RP, like my personal version of Leatherhead, named Spike, and the universal concepts.
So the general basis of the AU is that their entire universe was created by Sovereign Caelus, one half of the original universe. Caelus has a fascination with fighting, war, and death, being the "bad half" of the original universe creator. So, when Caelus took power, it allowed for all the bad things to take over. This causes a lot of changes to the source material, such as Splinter being a controlling, manipulative, and abusive "caretaker" while the boys are growing up. I'll do in-depth changes in a different post to keep myself organized.
The guys run through the war and apocalypse per the usual with these changes until there's a universal reset caused by the activation of the Apocalypse Protocol brought on by the Destroyer that resides in Donnie, World Ender (apt name, I know.) And the reset is carried out by the other Destroyers. This allows for the opening of the timeline where Mikey saves Casey Jr., which in turn sends Casey and Spike back to the past to save the future.
When Leo gets out of the Prison Dimension, he comes out with another person, Future Leo, in his subconscious. So that starts post-movie stuff where they're trying to clean up the Kraang and also figure out what happened to Future Leo's brothers.
I'll probably make a masterpost for information when I get around to it. I have to organize my ideas and write out general explanations for things, like the branches and the multiverses and their creators, the Destroyers. It's a lot.