- Major Characters: Raphael, Casey Jones, Leonardo, Michelangelo, Donatello, Old Hob
- Minor Characters: April O'Neil, Splinter,, Baxter Stockman, Chet
Cornered in the park, Raph and Casey are approached by the gang's leader, Old Hob. The sight of Hob triggers a repressed memory in Raph, who recalls Hob (as a cat) trying to eat him before getting attacked by Splinter. Casey tells Raph to snap out of it as the gang moves in under Hob's orders to pulverize the two.
Fifteen months ago. At Stockgen labs, Baxter Stockman gets a damage assessment from Chet regarding the ninja break-in. Though the terrapin exo-suit armor samples remain, the psychotropic serum was lost with Splinter and the traces of super soldier mutagen recovered from the alley have been tainted beyond use. Baxter is infuriated, as the ninja belonged to a rival of General Krang, who provided him with his secret mutagen at great risk; Krang won't like this news one bit. Chet suggests that if they can find Splinter, they can regain both the psychotropic drug and the mutagen from his blood. Baxter laughs at the idea of tracking down a single rat in New York City, but a slimy, furry, one-eyed individual comes crawling into the lab, assuring them he can do it: Old Hob.
At a police station, April tries to explain the ninja break-in to the cops, who are reluctant to buy her story. While relating the events, she recalls that it was Splinter who pulled the fire alarm and saved her life. Meanwhile, down in the sewers, the now-mutated Splinter tells his three Turtle sons to hurry up and make some distance between themselves and the lab. The Turtles recognize Splinter as their father, but don't remember their previous lives. Splinter explains that all will become clear in time and decides that their new lives requires new names, so he gives them the ones April had ascribed to them: Leonardo, Donallo and Michelangelo. More importantly, though, they must find their missing brother, Raphael.
Back to the present, Casey and Raph (who doesn't know he's Raph) are holding their own against Hob's thugs, but the numbers eventually overwhelm them. Casey is taken down by a brick to the head while Hob pistol-whips Raph into submission. Hob is about to blow Raph's brains out when a series of shuriken strike him in the arm. The other three Turtles have made it just in time and demand Hob back off. Hob isn't about to go back to Stockgen empty-handed and savagely attacks Raph while the other Turtles deal with the last of the gang. Raph pummels Hob and is only prevented from killing him by Leo. The three Turtles tell Raph his name and memories come flooding back. Momentarily, Casey recovers and is shocked to see four mutant Turtles instead of the one.
Down in the sewers, Raph is finally reunited with his father. Giving Raph a hug, Splinter announces that now things can truly begin...