In the future, NYC is ruled by Oroku Hiroto, grandson of the
Shredder and son of
Karai, who runs the city with meticulous fascist totalitarianism. A lone turtle, haunted by hallucinations of his deceased brothers, works to end Hiroto, whom he blames for his brothers' deaths. He traverses through the now heavily guarded NYC, fighting against synthetic ninjas (dubbed Synjas) on his way to the Foot Clan headquarters. He crashes out of the building, having failed his mission, and retreats into the sewer as a teenage girl called Jones follows. She finds the turtle attempting
seppuku before passing out from blood loss, and wakes up to see an older
April O'Neil, who identifies the turtle as
Michelangelo. Flashback sequences in sepia and in the style of the original Mirage comics reveal the events leading up to the present. After Shredder's death, the Turtles and the Foot Clan initially made a truce, but it fell apart when Karai tried to end the conflict between their families once and for all. An ambush leaves Splinter severely injured, and an enraged Raphael confronts Karai in an attempt to kill her, but Raphael is stabbed in the neck, and Karai is put in a coma from the fight. Baxter H. Stockman sends an ambush to retrieve Professor Honeycutt, which kills Leonardo and
Casey Jones, and a deceitful peace meeting set up by the Foot Clan has Donatello and Splinter killed as well. Mikey left NYC and lived in solitude for years, accompanied by Splinter's journal, but a fight with a gang makes him realize that it is his duty as the final remaining member of the Hamato family, the Ronin, to kill Hiroto. Mikey catches up with April and meets her daughter, Casey Marie Jones, who is part of a small resistance movement and is training herself to fight the Foot Clan. As Mikey grapples with his feelings on the resistance movement, Casey Marie's inexperience, as well as his advancing mutation, Hiroto puts the entire city under Martial Law in order to wrestle more control over it, which forces Casey Marie to gather resistance forces to stage an assault on Baxter Stockman's Fortress to disable the technology used by the Foot Clan. April, Casey Marie, and Mikey retrieve Professor Honeycutt's remains to kill Stockman and trigger a power outage throughout the city. The power outage causes a flood in the sewers, threatening to drown the resistance members and April. April reveals to Casey Marie that Casey is a mutant because of the former's prolonged exposure to the mutagen in the turtles. While Casey Marie tries to stop the flooding and rescue her mother, Mikey confronts Hiroto, who kills Karai and is now equipped with a special metal suit, and they both engage in a battle. They both land in the city outskirts, where Hiroto electrocutes himself and mortally injures Mikey, prompting Casey Marie and April to bid him farewell as he dies. As Mikey reunites with his brothers, Casey Jones, and Splinter in the afterlife, Casey Marie begins raising a new generation of mutant turtles to train them in the ways of
ninjitsu. ==Development==