I like the idea of Donnie building a robo-Raph mech.
Completely Turtle but not only his brand logo but but a set of bright red wings on the Mech for Red Angel.
Since all Hamato are dead minus CJ who's been accepted into that family and unknowingly restoring the Ninpo.
Originally Raph's spirit was supposed to possess the mech, now he's alone with the spirits of his dead family and humanity gone... leaving.
Him.
Alone.
Raphie goes Savage, he goes after anything and everything Kraang.
The other two remaining Kraang (I will never let the "Donnie closed the gateway while destroying their ship and killing the short Kraang but sacrificing himself" Die)
Didn't win thank to Raph being able to use everyone's Ninpo at once.
Now there's no one, only Raph.
Raph can't pass on.
Most of the Hamato clan leave except Donnie, April, Mikey and Leo realizing what just happened.
(Edit: Cassandra's ghost is following her son)
He's stuck as a mech.
Donnie breaks down and apologize.
Karai, Splinter, and Barry can visit but can't stay for long.
Big Mama watches over them but can't interact.
Raph spends his days creating piles of skulls and burning bodies, watching as the world slowly healed.
Watching over the entire world, waiting for... anything.
Traveling.
Though upon his return to New York, he's greeted with new and old faces.