Codename Unstoppable: The Mutagen Bomb Story is a fanfiction story written by Mewtwo Saki, and published at Fanfiction Net on 27 September 2018.
The story takes place in the 2012–2017 Nickelodeon series. It explores the events leading up to the Mutagen Bomb in the future storyarc.
The story starts out with the turtles hanging out in their lair, when they are approached by Bishop and Jack Kurtzman, who give them info regarding a potential last Kraang hideout, who are now only a shadow of their former selves. The turtles, along with April and Casey, then go to investigate the new secret operation of the Kraang, "codename unstoppable", in what is now the ruins of the Technodrome under the ocean.
Meanwhile, Karai plans to disband The Foot Clan, because of their violent legacy. She ponders on the decision for a bit, but is later attacked by a number of robotic Foot Soldiers. These Foot Soldiers are led by a figure who wears the armour of the Shredder, and the large amount of resistance forces Karai to take refuge in the turtles' lair, where she meets Shinigami, who had returned from Japan recently.
However, it is then revealed that Shinigami was a central figure in the resistance all along, immediately killing Karai and revealing her secret loyalty to the Shredder. Wearing the Shredder's armour, she and her Foot Soldiers wait in ambush for the turtles in the lair, who soon arrive from their mission against the Kraang. There, Shinigami quickly defeats them in battle but spares their lives, intent on prolonging their suffering.
The turtles, April, Casey, and their allies then escape New York City, which is being invaded by an extra-ordinarily large number of Foot Ninjas. They take refuge in the Northampton Farmhouse to reconcile with Karai's death, and Shinigami's betrayal.
Soon afterwards, a shared dream experienced by the turtles, as well as a tv broadcast by Shinigami encourages them to go back and put a stop to her reign of terror. After heavy resistance, the turtles and their allies manage to infiltrate the Foot Headquarters, where a battle between Leonardo and Shinigami in her Shredder armour ensues. However, after Leonardo decapitates his opponent, it turns out that the Shredder was a robot carrying a bomb, which then immediately explodes, destroying the building and seemingly killing everyone inside.
The story then cuts to Bishop, who cuts one of his Kraang-hunting missions short because of the news about the Foot invasion. Arriving in New York, he witnesses the explosion, but refuses to believe the turtles' deaths after failing to find their corpses among their allies' dead bodies.
After spending months doing research, Bishop manages to find out that Shinigami is still alive, hiding in what remains of Oroku Saki's final hideout in the middle of the woods. There, Bishop and his EPF defeat waves of Foot Soldiers before finally capturing Shinigami. Bishop intends to interrogate her, but instructs his EPF to immediately evacuate the area after he recieves a phone call which reveals that the Kraang are on their way to reward Shinigami for her support.
Bishop and his EPF then leave, with Bishop apparently becoming confident from the conversation that the turtles are still out there, alive. Soon after their departure, the Kraang then indeed arrive in large numbers, but kill Shinigami as they only saw her as a pawn in their greater scheme to use the Mutagen Bomb.
Meanwhile, the turtles wake up in an Oasis, 50 years in the future, where they learn that Renet saved them last second from the explosion, because they were are needed for the past, and that during their time in New York, Shinigami was supplied by the Kraang in order to draw the attention of the turtles, as well as the authorities, away from the Mutagen Bomb scheme.
The turtles then take up this mission, arriving in Dimension X thousands of years before the present day. After almost dying from the Dimension's harsh climate, they are saved by a much younger Bishop, who does not recognize them. After awakening, the turtles learn that Kraang-Prime is at the height of his power, and that Kraang-Subprime is still allied with his brother Bishop, albeit with hidden intentions. After failing to convince Bishop of his brother's evil, the turtles are kicked out from Bishop's residence.
Not willing to give up yet, they secretly follow Kraang-Subprime to a Technodrome that harbours Kraang Prime. Here, they witness the evil duo destroy the Triceraton Homeworld, as well revealing his plans of world domination, which involve using a Mutagen Bomb and getting rid of the Utrom High Council.
With this information in mind, the turtles then decide to split up in order to take care of the dire situation. Donatello and Michelangelo would infiltrate the Technodrome directly in order to foil Kraang's Mutagen Bomb plan by retarding its development, while Leonardo and Raphael headed back to the Utrom headquarters in order to save Bishop from a planned ambush by Kraang-Subprime. Both plans succeed, albeit with great difficulty and a little help from Sal Commander and his army, who are also brought from the present day. Re-uniting at last, the turtles escort a grateful Bishop to safety, after which Renet takes them back to the present day.
Back in the present day, the turtles and Renet, now joined by allies across dimensions (their 80s counterparts, Usagi, The Utrom High Council), foil a last ditch attempt by the Foot Clan to rise in power once more, led by Kraang-Subprime who manipulates them by falsely claiming that Bishop killed Shinigami. The turtles and their allies then regroup at the EPF headquarters, where they meet the present-day Bishop, who once again thanks them for their help in the past, and devises a plan to stop the Kraang once and for all.
The turtles, Bishop and their allies then head out into the now-ruined streets of New York, where a great battle between them and the Kraang army ensues. During the battle, Bishop recieves a message from his brother, who taunts him with the threat of a once-again perfected Mutagen Bomb. Bishop then leaves the scene of the battle in order to confront Kraang-Subprime, while the turtles and their allies continue the fight. They are almost defeated by the sheer number of Kraang droids, until Fugitoid arrives in a newly built Ulixes, wiping out the Kraang force.
The Fugitoid offers to take the turtles and their allies onboard, so that they can save as many people as possible before the Mutagen Bomb detonates. The turtles 80's counterparts, Renet, Usagi and the Utrom High Council take up this offer. However, the turtles stay behind, out of loyalty to Bishop and out of hope that the planet can still be saved. They then make their way to the Kraang headquarters, only to be stopped by Kraang-Prime, who finally founded them after having killed Sal Commander and his army. The turtles then fight Kraang-Prime in a long and drawn out battle, where they end up killing him, despite Donatello in particular suffering heavy injuries.
Meanwhile, Bishop managed to break into the Kraang-headquarters, making his way through a lot of resistance and attempting to defuse the Mutagen Bomb. However, he was then interrupted by Kraang-Subprime, who engages him in a one on one battle. Bishop emerges victorious from the battle and imprisions Kraang-Subprime in order to prevent him from intefering with the defusal of the Mutagen Bomb.
However, Kraang-Subprime then learns of his master's death from Bishop, and the rage that follows, gives him the strength to break free of his prison, and then defeat Bishop in an instant. He then stops the Mutagen Bomb from being defused, causing to explode and cover the entire planet, albeit in an imperfect state.
- A sequel to the story was eventually created and then completed, simply titled 'The Mutagen Bomb Story: Part 2". It takes place 50 years after the Mutagen Bomb explosion, detailing the lives of the turtles and their new friend Mira after they found Oasis in the Nickelodeon series.