Intro: Raph narrates as the Turtles battle a gigantic Nano monster in a spooky old amusement park at night.
Act 1: It's morning in the TMNT lair and April discovers that someone has used the last of her toothpaste - again. Frustrated, April walks out of the bathroom and into the main living quarters, where she's almost run over by Mikey on his new flying skateboard. Mike zooms around the living room creating typical mayhem until Raphael grabs the board and tosses him off - right on top of April! Raph apologizes to O'Neil and she storms off to find Donatello, admonishing him for using the Utrom technology to make Michelangelo a flying skateboard. Don shrugs and states that it was the only way to get Mikey off his shell, and then he puts on some diving gear and jumps into a pool - splashing April in the process. O'Neil is doused with water, which she thinks came from the sewers, but Donatello explains that its actually sea water from the bay. April isn't comforted by this news. Casey Jones arrives and O'Neil is overjoyed to see another human. Casey explains that he's off to do some late night repair work at the local amusement park, and he invites April along - both stressing that it's not a date.
Cut to the Coney Island amusement park, where we see the Nanobots emerge from a junk heap and rebuild themselves into a kid-sized robot. The reborn Nano spots a TV, repairs it, and sits down to watch 1950s sitcom that features an idealized version of the American family. The local news breaks in and reports that Harry Parker is being transferred to a new prison. Nano recognizes the thief as the man that it considers to be its "daddy" and heads out to find him.
Cut to Harry in prison, where he's cheating other prisoners in a card game. As Parker tries to gather up his ill gotten gains, an ace of spades falls form his sleeve, revealing that he hasn't been playing fair. The other convicts stand up and prepare to pummel Harry, but Nano shows up in the nick of time in the guise of a spider-like TV robot. Nano approaches Parker, who backs away in terror, but the Nanobots use the picture tube to create a smiling face that Harry recognizes as his old partner in crime. Prison guards rush in and Parker tells Nano that they're bad men holding him here against his will. Nano absorbs nearby vending machines and all other available hardware, growing in size. The robot grabs Harry and stuffs him into its chest cavity, and then breaks out of the jail.
Back at the Turtles' lair, Casey arrives to pick up April. The affable mechanic has brought O'Neil a bouquet of flowers - which unfortunately took a beating on the motorcycle ride over. April smiles and takes them, saying it's the thought that counts. The TMNT and Splinter tease Jones about when he'll be returning O'Neil home, and both Casey and April insist that it isn't a date.
Act 2: The Turtles are watching the news and learn about Harry’s escape and the return of the Nano-monster. Don wants to help Nano, and explains that its an innocent victim of bad "parenting", using the example that if Splinter had been evil, the Turtles themselves would have been raised as villains. Thus the TMNT decide to help the hapless Nanobots. Don jumps onto his computer and uses it to super-magnify and old video file of the miniature robots, where he discovers a patent number. Donatello goes online to find out who holds the patent, as he believes that Nano may be headed there.
Nano, meanwhile, breaks into the laboratory where it was created and kidnaps Dr. Richards, the woman who had been working on the Nanobot experiment. Nano calls her "mommy" and then stuffs Richards into its chest cavity, where she meets Harry Parker. The scientist unhappily recognizes Harry as the criminal that's escaped form prison. As the two bicker, Nano absorbs available hardware and assembles a makeshift version of the home that it had seen earlier in the '50s sitcom - right down to a couch where it sits Harry and Dr. Richards, stuffing a newspaper and knitting kit into their hands. Nano turns itself into a "child" and recites the same dialogue that it had heard in the TV show. Harry surmises that Nano has gone a little bonkers, and he and Dr. Richards begin to argue. The argument enrages Nano, as it wants nothing more than a happy family. The 'bot yells at its "parents" to stop fighting and creates menacing spikes that close in on Parker and Richards. The captives beg for mercy and then Nano comes up with another plan - it will take them to a happy place.
Act 3: Casey and April are at Coney Island, where the owner locks up for the night. Jones climbs onto a box and tells O'Neil that she'll enjoy the view from the top of the roller coaster. April says that they're supposed to be working, as Casey loses his balance and falls from his perch, landing on April. As Jones steadies himself by holding onto O'Neil's shoulders, the two gaze into each other's eyes and then lean in for a kiss - until some noise interrupts them. April asks what it is, and Casey replies that he didn't hear anything. However, the noise increases as Nano crashes through the front gate.
The Turtles locate Dr. Richard's lab and pick up Nano’s trail.
In order to make its “father” happy, Nano grabs the loot that it had stolen with Harry its first time out (which it had stored on a "Family Fun" display in the amusement park so all families could enjoy it). Harry is happy to see his treasure and asks to be let go, as does Dr. Richards. Nano gets angry and begins smashing up the park.
As Casey and April wonder what to do about the robotic menace, the TMNT drive up in the Battleshell. The Turtles try to reason with Nano, but the robot remembers them as the creatures that attacked it and thus it begins absorbing hardware from the park, growing to monumental size! The enormous robot tries to smash the Turtles!
Act 4: Donatello decides the way to beat Nano is to interface his laptop with the roller coaster’s operating system and then create an electromagnetic pulse that would “shut down” all the Nanobots that comprise the Nano-monster. Thus Don and April go to work on the coaster while the others distract Nano. Raph is briefly captured, but Leonardo saves him. Don manages to create the polarity field on the coaster tracks, and Mikey uses his flying skateboard to lure the giant robot to the ride. As Nano gets close to the roller coaster, the magnetic fields engulf it, and an electromagnetic pulse roars down the tracks and smashes into the titan's body, causing it to short out and collapse. As the smoke clears, Harry Parker and Dr. Richards crawl out from the rubble, unharmed. The Turtles watch Nano's view screen as the tiny bots flicker out of existence.
The police arrive and arrest Harry, who tries to convince them he didn't escape, he was kidnapped. The Turtles give the stolen loot to April so that she can turn it in for the reward money and rebuild her building/business. Donatello sheepishly kicks the ground and says that they probably won't be seeing April very much now that she has the means to leave their lair, but O'Neil rushes over and kisses him on the cheek, telling the Turtle that they'll see her all the time, because they're family.