Intro: Raphael narrates as we open with him running through the shadows of an alley being chased by an angry mob.
Act 1: Open in the Turtles' lair where we see Don and Leatherhead hooking up some electronic equipment. Michelangelo enters the room and slaps an antenna set on Leatherhead's scalp, asking the mutant gator to move around until a clear TV picture is tuned in. Donatello tells his brother to be patient, as the communications and entertainment system will be ready in a few minutes, but the impatient Mikey wants to watch TV right now. Mike manages to anger Leatherhead, who nearly flips out, but Don calms down his scientific friend in the nick of time. Master Splinter enters the room and tells Michelangelo that it's time for them to check the damage in the sewers caused by the Triceraton invasion - a mission that will give the Sensei a chance to try to teach the irascible Turtle how to connect his mind to his body and focus his energy more effectively.
On the surface, Leo and Raph are helping Casey Jones and April O'Neil board up her shop. As they finish and April turns her attentions to Casey, Raph and Leo decide to race home.
Mike and Splinter are investigating the sewers. The two are forced to surface when they come upon a passageway blocked by a cave-in. As the mutants emerge from a manhole and run along the streets, they are watched by two well-dressed men on a rooftop. We learn that the men are named Mr. Go and Mr. Touch. The pair knock their fists together which causes brilliant energy to crackle around them both - giving Mr. Go super speed and Mr. Touch super strength.
Act 2: Splinter sniffs and notes that they are being followed, so he and his son retreat into a nearby manhole. Soon after, the men who were spying on them follow. Mr. Touch is quite large and won't fit down the hole, so he rips open the pavement to enlarge the passageway.
As they transverse the sewer, Splinter and Mike are suddenly attacked by Mr. Go, who has a lead on his partner thanks to his super speed. Mr. Go is incredibly fast, and he manages to strike Master Splinter in the leg, dealing the old rat a painful injury that hinders his combat abilities. Mikey leaps in to protect his Master and Go focuses his efforts on the Turtle. Fortunately for Mikey, his plastron (the shell that covers his torso) protects him from the onslaught of punches that he receives. Mr. Go's "battery" of super powered energy is exhausted in his efforts to defeat Michelangelo. No longer facing a super-powered foe, Mike is able to clobber the villain. As Mikey prepares to finish of his adversary, Mr. Touch arrives and punches the Turtle, sending him flying into a wall. Splinter assists his student to his feet as Touch and Go re-energize one another. As the villains close in on our groggy heroes, Splinter leaps up and kicks a weakened pillar, causing it to collapse. The Sensei pulls his son to safety as the ceiling collapses on Touch and Go. As soon as the dust settles, Splinter notes that their enemies are already breaking free of the debris, so he and Michelangelo retreat.
Leo and Raph continue their race along the city skyline. Raphael decides to take a shortcut, but as he changes his course, he steps on a damaged ledge and it breaks away. Fade out as Raph is falling towards the ground.
Act 3: Still falling, Raphael grabs a flag pole to slow his descent and then grips a street light and swings around twice until his momentum is reduced enough to allow him to land safely on the street. Unfortunately Raph barely gets his bearings when an angry mob spots him and begins to give chase, assuming that that the Turtle is one of the invading aliens.
Raph runs down a dead end alley - his only escape route is a locked door. As the mob closes in and the ninja prepares to fight, the door suddenly opens and a blind old lady comes out. The woman mistakes Raphael for a boy that was supposed to come over and help her. Raphael is all to happy to escape the mob and he enters her apartment.
Cut back to Splinter and Mike, who are trying to escape through a subway station - but the doorway is locked. Touch and Go arrive and the fight is renewed. Things do not go well for our heroes, but Mikey gets an idea that requires distance between themselves and their adversaries.
Raph is inside the old lady's apartment, helping her move large boxes. Raphael learns that her name is Mrs. Morrison and she is being forced out of her home by the bank, as she has run out of money since her husband passed away.
Cut back to Mike and Master Splinter as Touch and Go have them backed up to a subway track. The mutants are tossed down onto the tracks just as a train arrives. As the subway cars fly past, Touch and Go see Mike’s nunchakus and Splinter’s robe and cane lying on the tracks.
Act 4: Open with Mr. Touch and Mr. Go as they hold Splinter and Mike’s things, thinking that they’ve killed the mutants. The villains take the items and head out to report to their employer.
Back at the Turtles' lair, Leonardo arrives and asks Leatherhead and Donatello if they've seen Raph, as he's very late. No one has seen the hot-headed ninja.
As it turns out, Raphael is having a cup of tea with Mrs. Morrison and her pet cat. Raph has quickly made two new friends.
Touch and Go enter a large hotel suite. Hun is revealed to be the one who hired them to kill Splinter and the Turtles. While Touch and Go are being paid with a briefcase filled with cash, we hear Mikey calling out from the hallway,“Room service.” Hun snarls that nothing was ordered but Mikey is insistent, so the criminal hulk angrily opens the door. Mike attacks with a push cart, sending Hun flying into the room where he lands unconscious on top of Mr. Go, pinning him to the floor. Michelangelo then engages Mr. Touch in combat, making sure to stay out of the super villain's way as he expends his energy on ill-timed punches. Splinter uses an extinguisher to create a thick fog in the room, giving the ninjas the advantage. Mike knocks the three villains through a window - Touch and Go crash into the sidewalk far below while Hun manages to helplessly hang on to the window sill.
Mikey grabs a briefcase filled with cash and thanks Hun for the donation. As Michelangelo and Splinter look down, they see that Touch and Go are gone. The police cars begin to arrive, so Splinter and Mike leave, taking back their belongings and the suitcase full of money.
Cut to Turtle Lair where Raph has finally arrived. Mike and Splinter also make it home, and the Mikey reveals the contents of the briefcase. As Michelangelo ponders how they'll spend the money frivolously, Raphael gets an idea.
Later, at Mrs. Morrison’s apartment, Raph rings the doorbell. When the kindly old lady answers the door, the ninja hands her the briefcase filled with cash, telling her that someone left it on her doorstep.