Intro: Michelangelo narrates as we open with the four Turtles, Casey Jones, and an old superhero named Stainless Steve Steel. They are wearing high-tech domes on their heads as they sneak past tons of small robots with the same type of domes. Entering a room holding a bunch of shadowy figures trapped in containers, Stainless Steve begins to break one open. With this we see a giant shadowy figure explode through a wall advancing toward the group.
Act 1: Mike is reading (out loud and using different voices) a comic about a group called the Justice force and comes to the end where a character named Battling Bernice is zapped by a ray gun. Needing to know if she survives, Mikey scrambles through his collection tossing issues around and disturbing Master Splinter's meditation. The Sensei tells his son to quiet down as Mikey frantically dials the comic shops in NYC seeking the missing comic book. The other Turtles arrive and create more noise, upsetting Master Splinter who orders them all to practice their ninja art of silence for one hour. Just then, Casey Jones walks in with a boom box on his shoulder blasting tunes - which is more than the wise old rodent can take and he orders them all to go outside.
Mikey explains his dilemma to Casey and Jones knows just the place to go - a comic shop in Northampton, Massachusetts. Thus the Turtles and Casey get on their Shell Cycles and take a road trip to Northampton in search of the comic.
Cut to Northampton as the guys arrive at Steve's Comic Shop. The boys go inside undisguised as it's "costume day" at the store. Donatello discovers a cool flying remote control toy of the Silver Sentry that he borrows money from Casey to buy. Mike asks Steve about the missing comic book and learns that the last issue was never made. However, the store owner tells the disappointed ninja that Bernice didn't make it. While Steve talks, a bunch of Domeoids (evil robots from the comic) crash through a wall, only these ones are real!
Act 2: As the Turtles battle the robots, we see a stock boy suddenly morph into the Justice Force superhero known as Metal Head. During the battle, Mikey tosses a Domeoid towards Steve and it strikes him in the head - causing the shocked Turtle to shriek. Fortunately the proprietor of the comic shop turns out to be none other than Justice Force team lead Stainless Steel Steve - the collision did him no harm as his skull is armor plated. Mike is delighted to discover that his comic heroes are real!
During the battle, the robots capture Metal Head and escape with him. Steve injured his back in the fight and needs to lie down on the floor. While prone, he explains that a former Justice Force member, Dr. Dome, went mad after the death of Battling Bernice and turned on the super team. Stainless Steel Steve then uses his Justice Force emergency signal to call the other members to his home.
Cut to Steve’s house. Leo discovers that the door is unlocked and our heroes enter cautiously. Casey spots a costumed man in a wheelchair and announces that it's just "some old guy" which upsets the former super hero, who uses his hyper-speed capabilities to spin circles around Jones, lifting him in the air and dropping him. Next we meet the stretching hero named Joey Lastic, who is having problems retracting his limbs once he's extended them. Steve dons his old costume and is given a super-massage from Zippy Lad, which makes the old time hero feel much better.
Suddenly, Domeoids attack the house via the roof. During a protracted skirmish, the robots capture both Zippy and Joey before escaping. Luckily, Don had planted tracking devices on the heroes so the Turtles, Jones and Steve are able to give chase.
Following the tracking signal, our heroes discover a giant dome fortress guarded by hundreds of Domeoids.
Act 3: Severely outnumbered, the team needs a good plan to gain entry. Don lures six robots away with the flying Silver Sentry toy that he bought at the store. The group uses the six dome tops they acquired from the robots to disguise themselves as Domeoids - apparently the red flashing prevents the pesky little 'bots from attacking one another, thus while not the greatest of camouflage, the disguises work and allow the team to gain entry into the Domed Fortress.
As our heroes enter the lab room, they find where Metal Head, Zippy and Joey are being held captive in stasis tubes. Steve breaks out Metal Head, but before he can free the others, a giant mechanoid controlled by Dr. Dome crashes through the wall and attacks!
While Dome and Stainless Steel Steve battle one another, we discover that the once-good Doctor thinks that Steve and the Turtles are the ones who captured the other Justice Force members. Steve argues the point, so Dome frees Zippy and Joey to get their stories.
Still confused from both men's argument, the two sides battle on as Domeoids flood into the room attacking everyone. With this a costumed woman bearing a striking resemblance to Battling Bernice arrives. Dr. Dome monetarily thinks that Bernice has finally returned, but when he realizes how young this lady is he knows that can't be the case. The woman reveals herself to be Bernice’s daughter, Ananda. She blames all of the Justice Force for the demise of her mother, and thus she plans to destroy them in a fit of revenge. When the team wonders how the villain is able to control the Domeoids, Ananda reveals that she is Dr. Dome’s daughter as well, and she has inherited her her father’s mental powers. With that explained, the Domeoids begin to attack all of the shocked heroes.
Act 4: Ananda and her army of robots successfully capture all of our heroes. Things look grim until Dr. Dome focuses his energy and briefly gains control of the mechanical menaces, freeing everyone. Ananda then refocuses her powers and short circuits her father's brain, regaining control of the horde and sending them back into battle.
Mike comes up with a plan: the heroes split their attacks in many directions to confuse and overload Ananda's mental capabilities. The plan works! Ananda loses control and Dr. Dome's giant mechanoid falls onto her legs, pinning her to the ground. Dome takes control of the monstrous robot and frees his daughter - the old man helps her to stand and takes her hands in his, and explains that while she has lost her mother, she still has a father who wishes very much to be part of her life. The two make peace and hug.
Outside the Domed Fortress, the old-time super heroes thank the Turtles and Casey for their help. As the others ride off, Stainless Steel steve calls out to Mikey and congratulates him for coming up with such a great plan and asks how he came up with the strategy. The young Turtle reminds the senior citizen super dude that the same thing was done in an issue of Justice Force. The Justice Force members smile as Steve tosses Mikey his own Justice Force emergency call signal, thus making the ninja an honorary member of the super team. Mikey is delighted and he races off into the sunset to catch up with his brothers.
Cut to freeze frame of screen as it pulls back revealing it to be the final page of the final comic book that Mike had been searching for in the beginning. As we view the cover, we see Mike is part of the Justice Force and he is very satisfied.