Some TMNT stuff really isn't for little kids.
- Story: Kevin Eastman, Bobby Curnow, & Tom Waltz
- Script: Tom Waltz
- Art: Mateus Santolouco
- Flashback Art: Cory Smith
- Colors: Ronda Pattison
- Letters: Shawn Lee
- Editor: Bobby Curnow
- Donatello / Metalhead
- Hamato Yoshi / Splinter
- Oroku Karai
- Oroku Saki / The Shredder (death)
- Angel Bridge / Nobody
- Zayton Honeycutt / Fugitoid
- Harold Lillja
- Krang (Flashback)
- Masato (Flashback)
- Sulfurch (Flashback) (debut)
Splinter commands his sons to not let their enemies dictate the fight, and reminds them that if they control themselves they will also control the battle. The Turtles lunge into the fight as a team, while, Splinter meditates and remembers the day when he and his sons died in feudal Japan, and then goes further back into memories of his arguments with Oroku Saki.
On Burnow Island, a mysterious scaled figure assists Professor Honeycutt in administering ooze to Donatello's comatose body.
Raphael and Michelangelo begin working together to pit Rocksteady and Bebop against one another, while Leonardo gets the drop on Koya and begins slicing off her flight feathers. Bludgeon, who is attacking Donatello, is distracted at a crucial moment and Donatello takes the opportunity to blind him. The two crippled mutants leave the Gauntlet, but that still leaves Bebop and Rocksteady, who are still crashing into each other due to Michelangelo and Raphael's maneuvers.
Suddenly Donatello responds to a voice that isn't there, bids farewell to his brothers, and initiates the robot body's autodestruct sequence. His friends and family are horrified as the Metalhead body explodes, knocking Bebop and Rocksteady off their feet. But suddenly Donatello is right there in the flesh, with a new metal shell and a metal bo, and he finally finishes the fight by knocking both enemy mutants out. His brothers and father embrace him.
Splinter tells them that they will have to keep fighting without him a little longer, as he hasn't been able to figure out a way to defeat Shredder. Shredder chooses to fight the final battle on the rooftop, where he prepares to fight the four Turtles. They each are able to land hits on him, but he fights back with more strength and skill than they can win against - he grabs Leonardo by the throat, flips Donatello with his own bo, stabs Raphael in the leg with his own sai, and even Michelangelo flies at him, screaming that he's sick of Shredder hurting people.
As they fight, Splinter's mind flies back all the way to when he and Saki were boys, and Masato was lecturing them on their personal flaws. Finally he rises and knocks Shredder backwards. He uses the fallen weapons of each of his sons to lash out at his old enemy, even as he explains why he's chosen to live his life as he had, which enrages Shredder. Finally he lands a mortal blow with Leonardo's katana, and Shredder collapses to the floor.
He removes Saki's helmet, and his onetime friend pleads that they were once like brothers, but that Yoshi turned his back on him. Splinter said he is sorry that he accidentally turned his back not only on what Saki had become, but to him himself. They reminisce about their boyhood dreams of warrior honor for a moment, before Shredder pulls open his shirt and prepares to commit seppuku. He says farewells to Karai and Kitsune - not fully accepting death right to the end - and swears that he will see Yoshi in the forest once again someday. Shredder stabs himself with his blades, and Splinter slices off his head.
Karai comes forward and says that she has seen true leadership in the Gauntlet, and that she must now return to Japan and look to the past if she can ever become a leader like Splinter is. So she offers her grandfather's position and sword to the mutant rat. Splinter accepts.
Michelangelo, who was already horrified by Splinter's part in Shredder's death, drops his nunchaku and declares that he can't be part of this. Leonardo tries to reason with him, but he leaves.
Splinter picks up Shredder's helmet and reminisces again about when he and his old enemy were boys, before declaring that he and the Turtles will embrace their destiny.
In an epilogue set in feudal Japan, an Utrom named Sulfurch surveys the hillside where Hamato Yoshi and his four sons were murdered. He's commanded to send Chief Science Advisor Ma'riell to take DNA and QNA samples from the dead bodies, in hopes that it can be used as an advantage someday. It's then revealed that the speaker is none other than Krang.