Intro: Open in Cody's penthouse where we discover that Mikey has been up for forty-seven hours finishing his favorite new video game, "Helix". Cody has also been up working on some type of project, but all we can make out is a chrome hokey mask.
Act 1: After Mikey finally beats his game of Helix, he clicks the television to the morning news. Coincidentally, there's a live broadcast that explains the new Helix Two game is arriving at stores in the Levellex Mall that day - huge crowds are already lining up. Mikey thinks it's the best day ever and wants to go. Cody states that the mall is beyond huge so they'll need some help navigating it. Jones calls Starlee and she agrees to the "date".
Cut to the city streets where three delivery trucks hauling the hot game are being escorted by the police. Suddenly, Jammerhead and his Street Phantom gang members appear and try to steal the games. Jammerhead takes control of a police robot, but the trucks are protected by force fields, thus the villains can't gain entry. The thugs decide to stow away onboard a police car and wait until the trucks drop their shields at the mall to make their move.
Back at the penthouse everyone is ready to go except Cody (who would rather be working on his secret project). After some prodding by Master Splinter, Jones reluctantly agrees to make the trip. The four Turtles, Cody and Starlee hop into the Hovershell and fly off to the Levellex Mall.
Act 2: The Turtles and their friends reach the mall and find a huge line in front of the store. Mikey and Cody enter the long line (much to Starlee's disappointment, as she wanted to spend time with Cody) while the others decide to hit the food court.
Meanwhile, the delivery trucks arrive at the loading docks of the mall. All looks clear, so the peacekeepers drive away. Jammerhead scrambles the security bot and then phases into the truck's cab, terrorizing the driver.
Inside the mall, Mikey decides to cut to the front of the line ninja-style. Just as the store opens, Mike and Cody sneak in. The pair soon hear strange noises coming form the loading docks and head out to investigate - where they discover that the Street Phantoms are robbing stealing the games! Mikey moves in and tells Jones to call the others - but Cody's communicator is jammed and won't work - so Mike is on his own!
Unfortunately there are too many Phantoms and they soon defeat Mikey by wrapping him in bubble wrap and trapping him with a forklift - thus the villains drive off with the delivery trucks and all of the Helix Two games!
Act 3: Open as the others finally catch up with a very angry Mikey. Mike is freed and the Turtles jump in the Hovershell and take off after the Street Phantoms. The swifter vehicle has no trouble catching up with the thieves, but to make matters worse, Jammerhead uses his electronic device to plug into the mall's security system and changes the video to make it look like the Turtles are the ones that have stolen the games!
The bogus security video is then broadcast on all of the monitors at the Levellex Mall - now everyone thinks the TMNT are crooks! Cody and Starlee realize their friends have been framed and try to come up with a plan to help. Jones, determined to get in on the action, uses his wrist communicator to activate the project he’s been working on and then disappears, leaving a confused Starlee alone in the mall.
Back at Cody's penthouse, Serling is unhappily cleaning up the apartment. The server bot is lost in his work and doesn't notice that the large white sheet behind him is covering Cody's project - which now springs to life and exits the building (draping the sheet over the bewildered Serling as it departs).
Cut to the Turtles as they manage to stop the stolen trucks by cutting them off. As our heroes are about to take back the games, Constable Biggles arrives with his team of peacekeepers. Biggles, thinking the Turtles are to blame, lets Jammerhead and his stolen merchandise get away while he tries to arrest Mikey. Mike goes bonkers, tosses around the officers and then takes off in one of the police cruisers! In the midst of the chaos, the other Turtles speed off in the Hovershell, hot on Mike's heels. Biggles orders his men to their cars and a chase is on.
Meanwhile, Cody has climbed to the roof of the mall, where he's met by a flying robot. Jones activates controls and the chest cavity of the machine opens - Cody climbs inside and zooms off into the skies!
On the streets below, the stolen trucks are in the lead with Mikey right behind them, followed by the Hovershell and then by Biggles and his crew. Jammerhead has an escape plan - as he reaches a barricade blocking traffic from falling into a large chasm in the road, the villain activates controls and a ramp forms in the middle of the roadblock. Jammerhead speeds over the ramp, sending the truck flying into midair, apparently trying to leap the deep ravine - but in the middle of the jump, the truck disappears! Back on the road, the Street Phantoms spill barrels of oil onto the streets. Mike spots the barricade and hits the brakes - but he begins to slide on the oil. To make matters worse - the Hovershell collides with Mike's cruiser and begins to push it towards the ramp, totally out of control and going too fast to stop either from falling!
Act 4: As the Turtles go skidding to their doom, a flying robot zooms in and braces itself against the cruiser, applying enough resistance to keep the vehicles from plummeting over the precipice. The rescuing robot is none other than Cody in his new “project”, the Turtle X. The TMNT regroup and Donatello realizes that the stolen truck didn’t just disappear - so he pole vaults into the air and disappears just like the delivery truck did! The others leap into the air just as Biggles and his officers arrive.
Our heroes find themselves on the deck of and on the ship that has a been using a cloaking device to hide its presence. Unhappy to have guests, the Street Phantoms attack. A battle ensues and the Turtles quickly gain the upper hand - until Jammerhead uses his device to scramble Turtle X's functions, sending Cody on a rampage that leads to the edge of the ship! Just as Jones is about to fall off the vessel into the chasm, Raph throws his energy powered sais into some containers. The containers explode, causing the Phantoms to scatter and destroying Jammerhead's device. Cody regains control of his bot and the ships cloaking device is knocked out, revealing it to the police. The Turtles jump back to the street and call out for Cody to do the same - but Jones decides to try to save the games. The Turtle X shoots a grappling hook onto the delivery truck and Cody tries to fly to the street, but the weight is too heavy and he falls, barely grasping the edge of the road. The TMNT tell Jones to drop the truck before it pulls him down, but Cody is reluctant to do so. Mikey leaps onto the Turtle X and tells Cody to drop the truck - it's just carrying games and it's not worth dying over. Jones disconnects the cable and the truck falls into the crevice.
The Turtles take off and Cody tosses Biggles a holodisc that reveals Jammerhead's confession that he set up the TMNT to take the fall for the theft. Happy with this, Biggles orders his men to arrest the Street Phantoms.
Cut to the penthouse where everyone is back safe and sound. Master Splinter is upset that Cody has gotten so involved with the action and tells him that he must not participate in combat until he is fully trained. Jones is visibly unhappy with this decree, but he seems willing to listen. Starlee enters the room and begins to yell at Cody, saying that he has some explaining to do. Jones tries to apologize for leaving her at the mall - but Starlee is actually interested in how he created the Turtle X. As the two begin to leave, Mikey swears off video games forever. Starlee turns around and holds up the bag she's carrying - wondering if she wasted her time picking up a copy of Helix 2. A green blur snatches the bag from her grasp and Mikey is once again off to play his favorite game.