At Channel Six, April's boss is on her case about the Turtles. He's convinced they're a menace to society, and wants April to expose them. Of course, April won't do so, and sets out to prove they're heroes. And as if that's not enough, while Master Splinter is meditating, he declares that he senses Shredder is coming back.

Shredder goes to the "Slash for Cash Dojo" and recruits the students in his plan. He trains the young students and when they're ready, he has them dress up like the Turtles, call themselves the "Crooked Ninja Turtle Gang", and has them go on a crime spree in the city. On one of these sprees, April and Vernon were there the catch the action. They see the "turtle" robbers, but April refuses to believe the Turtles did it. Meanwhile, Shredder calls Krang and tell him his plan: to ruin the Turtles' reputation so they have to surface to clear their names. Krang yells that he wants results now, so Shredder is left with only one place to turn...

In the Turtles lair, Splinter is abducted by a huge dirt-shoveling rat-catcher and driven off. The Turtles arrive later and follow the path the rat-catcher took, which leads them to a junkyard. The CNTG is there, and the Turtles make short work of them. They see a message Shredder left them, telling them to meet him at the "Slash for Cash Dojo". When the Turtles arrive there they see Splinter tied to the wall with a battering ram above his head. Just as Shredder is about to cut the rope and smash Splinter to bits, Baxter arrives with the rat-catcher to take care of the Turtles. The Turtles take care of him instead, wrecking the machine and causing it to go haywire. In the confusion, Shredder slices the rope anyway and runs off. The Turtles manage to get the machine under control and save Splinter in the nick of time.

April delivers the report that the entire "Crooked Ninja Turtle Gang" was a hoax, and the real Turtles were heroes. The Turtles sit at home watching the report, satisfied in a job well done.

The Turtles find the first fragment on a garbage barge, but then Shredder shows up and takes it. They engage in "clean" combat, to which the Turtles lose. Shredder holds up the first fragment and something strange happens. The Turtles starting shrinking! That was the power of the first fragment: it made things shrink. The Turtles barely escape becoming Ninja Turtle pancakes, and make it home.

Shredder calls Krang and tells him of the Eye of Sarnath, and how he shrunk the Turtles, but Krang doesn't believe him. Krang demands proof, so Shredder heads out to get him some. Once home, the Turtles explain everything to Splinter, who calls April for help. On April's way over, she sees the Empire State Building was actually shrinking! After the building was completely shrunk, Baxter Stockman, in disguise, comes to take the building away for "research". Once Shredder has the building is his hands, he calls Krang. Now he'll have all the proof he'll ever need!

April and Splinter finally make it out of traffic and to Shredder's hideout. Inside, Shredder is about to crush the Turtles with a crowbar, but before he can, Splinter bolts in and starts fighting Shredder. April manages to find the fragment and returns the Turtles to their normal size. Just as Shredder starts getting the better of Splinter, the Turtles come to the rescue. But during the confusion Baxter gets the fragment and the villians get away.

The Turtles head home, watch April on the tube, and eat dinner. All is well.

The worker at the aquarium leaves, but not before patting the Manta Ray goodnight. He's investigating possible illegal pollition coming from the sewer. He sticks his hand down into a green ooze in the water, and then a large burst of water carries him out to sea. Meanwhile, Shredder is planning the destroy the Statue of Liberty with a torpedo, which just happens to be heading for the Turtles. They escape, jump aboard the sub, hear of the plans, manage to get into a fight with Bebop and Rocksteady, which resulted in a hole in the side of the submarine. Shredder escapes, while the Turtle swim out. Meanwhile, a shadow attaches some explosives to the sub. It talks to itself, saying it must save Liberty.

Just as Shredder thinks he's gonna make a clean getaway, the shadow comes into clear view. It's a huge Manta Ray-Mutant Man who calls himself Man Ray (later to be Ray Fillet). Shredder and Man Ray fight, and Man Ray ends up taking Shredder to the shore. Shredder escapes, and Ray gets back into the water because he was so tired. The Turtles watch him go, and wonder about who he is. They turn around to watch the wonderful Fourth of July fireworks.

Leatherhead chases after Mary, but she disapears. Leatherhead crashes into Shredder's sewer hideout, and Shredder lies to him, telling him that Mary Bones and the Turtles are evil and that they hold the key to returning him to human form. Leatherhead agrees to capture the Turtles.

The Turtles end up fighting Bebop, Rocksteady, and Leatherhead on an old bridge. Leatherhead, being confused with the two conflicting stories, Shredder's and the Turtles', he throws a fit. When his tail smacks against the old bridge, a part of it collapses on Leatherhead. As our heroes make an exit, Mary Bones appears and gives them a strange message and vanishes. Raphael looks around and notices something shocking...

With no other choice, the Turtle agree. They are introduced to the other wrestlers, and are surprised to see Leatherhead is among them! The find out that Cudley had saved him from his deathly encounter with the bridge, and brought him there, to Stump Asteriod, to fight.

After alot, and I do mean alot, of wrestling, the Turtles end up victorious. Stump does as he had promised and has Cudley deliver the Turtles back to Earth.

For some odd reason, the Turtles take their own blimp, and it is also destroyed by Wing Nut. They escape, and Wing Nut chases them. Eventually, the Turtles confront Wing Nut on a rooftop, and are surprised to find out that Wing Nut and Screwloose are actually a pair of aliens from a world that Krang destroyed. Wing Nut was the last of his race, and this drove the poor bat-boy insane. Wing Nut and Screwloose are searching the globe, seeking revenge against Krang. Wing Nut, being slightly deranged, believes that Krang is hiding behind a skylight, and is breaking every one he can find, in hopes of finding the evil brain.

Eager to continue his search, Wing Nut escapes, but is soon gobbled up by Cudley the Cowlick. When Cudley brought the Turtles home, she accidentally opened a dimensional portal which allowed Wing Nut to reach Earth. Cudley returns Wing Nut to Stump Asteroid, where she hopes they will find a home.

Bebop and Rocksteady bring the agent to Shredder, who wants the stolen plans, but Chameleon hid them in the sewer, so he doesn't have them. Shredder demands to know where the plans are, so Chameleon offers to sell them to him. This angers Shredder, so he brings out a real live chameleon and a spray can of mutagen, explaining that if Chameleon doesn't hand over the plan, Shredder would mutate him into a real chameleon. Chameleon agrees, and tells Shredder where he his the plan. Bebop and Rocksteady rush off to get the plans, and Shredder, being the villian that he is, mutates Chameleon anyway. But once he's mutated, Chameleon changes his colors and escapes.

Meanwhile, Don is working on the weird Foot vehicle when Bebop and Rocksteady rush in, firing their guns. They each head for cover, and a shoot-out takes place. The Turtles thrpw their Shurikens, and Bebop and Rocksteady fire their lasers. Chameleon arrives at the shoot-out because that's where he hid the plans, and he gets Rocksteady and Bebop to fire at him, causing a cave-in above them. Bebop and Rocksteady are saved by hiding under the Foot vehicle, but before the debris hits the floor, Chameleon retrieves the plans from their hiding place escapes. With the tunnel sealed off, the Turtles leave, thinking that Bebop and Rocksteady were killed. The Turtles get home just in time to see April's report: the stolen weapons plans were mysteriously returned with a note saying, "Some thing are not worth profiting from."