He traverses through the now heavily guarded New York City, fighting against synthetic ninjas (dubbed Synjas) on his way to the Foot Clan headquarters.

Mikey left New York 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 get the remains of Professor Honeycutt to kill Stockman and send a power outage throughout the entire city.

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 to death and mortally injures Mikey, where Casey Marie and April bid farewell as he dies.

Andy Kuhn was set to be the original artist for the series, before being replaced with Esau and Isaac Escorza, with Ben Bishop joining the project to illustrate the flashback sequences.

Thematically, Mikey gave us the opportunity to explore the irony of the one person in the family who never truly bought into the clan-war aspect that exists at the foundation of their lives – being the only one left alive and stuck with the mission of ultimately winning said war, or dying trying.