New York was under the control of The Kraang, with the Shredder taking the handles from behind. The crew came back to find a city in ruins. As they were trying to find Splinter...

"Hey! There's someone there!" Mikey points out to an abandoned building, your hideout. Turns out they found you, their youngest sibling who they thought didn't make it.

But if you were alive... Then Splinter must've been able to make it too, right? The four of them ran to give you a hug, together at last...