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As time passes the Shredder begins to gain more power, humans are killed or forced to cower in fear at the might of the Foot Clan. April is forced to close the O’Neil tech building to assist in the resistance. A foot clan strike team eventually finds the Turtles lair and attacks, Splinter sacrifices himself so his sons can escape. The already strained relationship between Leo and Raph finally snaps with Raph accusing Leo of abandoning Splinter. Leo insists that they had no choice but to leave Splinter behind. Raph then shouts “Just like they didn’t have a choice in leaving Donnie behind!” This gets Leo riled up and the two brothers fight. In the battle, Raph loses his left eye, Raph damages both of Leo’s eyes, and Mikey’s arm is severed when he tries to step between them. The three brothers go their separate ways, but Mikey is able to keep in touch with them.
April’s children grow up and get married and she becomes a grandmother. Humanity continues to suffer at the hands of the Shredder. The Turtles as individuals take out the Shredder’s forces where they can, but their efforts are still not enough. However without actual proof that Donatello is alive or dead, the Shredder knows that the missing Turtle would be seen as a beacon of hope for his brothers if he reunites with them. So he does keep an alert out for someone matching Donatello’s description. Thirty years after Donnie’s death, a sixteen-year old version of Donatello appears in the future New York and is nearly arrested by the Foot Clan. He is found by Mikey who has become embittered over the years since his brother's disappearance and demands to know why he abandoned them years ago. When Donnie has no answer to his questions, Mikey sighs and tells him that it isn’t safe to be out in the open. He takes Donnie to Splinter’s grave and fills Donnie in on how Splinter died. Donnie is naturally upset that his father is dead and tells Mikey they need to get their family back together and make one last strike against the Shredder. Mikey takes Donnie to April and her resistance group. Donnie is surprised to see that Karai and Bishop are now allies. Leo and Raph are summoned and arrive, but when they see each other, old wounds are reopened and the two start to attack one another until Don reveals himself to them. They are surprised and glad to see him but reluctant to take on the Shredder since the last time they did so they failed and lost Casey as a result. But ultimately agree the Shredder needed to be stopped one way or another.
In the meantime, Khan reports to the Shredder and tells him that Donatello has been spotted in the city. Shredder knows this means that his enemies would attack soon and tells Khan to prepare for it, but he wants to destroy Donatello himself.
The turtles attack the Shredders strong hold, with April, Karai, Bishop, and Stockman. Donnie is wearing a modified exosuit to help with taking on the Shredder’s Utrom tech-armor. During the battle Stockman is destroyed, and Karai also is killed but not before the Shredder denounces her as a pawn who has long since lost any use. Khan is destroyed by April to avenge Casey. Leo, Raph, and Mikey are unfortunately overpowered and killed by the forces of the Foot Clan. Shredder slowly and painfully begins to crush Donnie’s exosuit. As he’s killing his prey he gloats that he expected more from him after thirty years and he should spend his final moments looking upon those he has failed. Donnie however states that he only needed to get in close before he presses a button that causes a chain to shoot out and wrap around Utrom Shredder's armor so that Donnie’s exosuit is pulling him into a big hug. The exosuit then self destructs and takes Shredder with it.
Despite the fact the battle is over, Donnie feels no sense of victory over what happened. April tells Donnie tells him he gave back a future to everyone else. As Donnie is summoned to back to his family, April tells him to believe there is always hope. She reports the death of the Shredder to the resistance and everyone rejoices at finally being free of the Shredders tyranny. O’Neil tech is reopened and helps rebuilding and restoring the city into the world the Turtles would discover in the year 2105. April passes on peacefully in her sleep, her eldest grandson is made the new CEO of O’Neil Tech and marries the sister of Darius Dunn. Darius plays the part of the loyal friend and worms his way to a position to be COO of O’Neil Tech. Cody Jones is born and often left in the care of Sirling while his parents are promoting and seeing to O’Neil Tech. Dunn arranges an accident for his Sister and his Brother in Law, he then takes an acting role as CEO all the while grooming and manipulating his nephew until he is of age, with the intent of eliminating him once he no longer served a purpose. Cody comes across his great grandparents journal and reads about the Turtles and becomes fascinated by them. Dunn chides his nephew about his obsession with the past. While looking through some of Donatello’s old blueprints he finds one for the time window and decides to build it so he can look back on the past and accidentally brings the Turtles and Splinter forward in time.
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