Intro: Open in a Manhattan post office in the year 1990. A disguised Donatello enters and hands the postmaster a letter with very specific instructions. It’s to be delivered to Michelangelo Splinterson, 131 97th street, Penthouse… for the morning of July 10th, 2105!
Act 1: Open as Cody and Don work on the Time Window in the lab.
Cut to Sh’Okanabo’s ship. Darius Dun contacts the evil alien to see how he's progressing with the stolen plans for Cody's time machine. Sh'Okanabo tells Dun that he will contact him when things are ready. Dun closes the connection and we discover that the villain's Time Window is finished! Viral activates the machine, but something goes wrong and the power surges, washing everything out with white energy!
Cut back to the lab where Cody, Don and now Mikey are working on the Time Window. Suddenly, a red warning light begins to flash as an alarm sounds. Cody investigates via the computer and discovers that there’s been a rip in time and space in the city, which can only be created by a machine just like Cody’s Time Window!
Cut to the streets of New Manhattan as Cody, Splinter and the Turtles race along on Shell Speeders and the Big Wheel. Time rifts to the past begin to open everywhere! The group tries to avoid the obstacles, but they collide with one another and go flying out of control! Don and Splinter are launched into one rift while Cody and Leo fly into another. Meanwhile, Raph and Mikey are left in front of a rift that has dinosaurs pouring out of it!
Act 2: Mikey and Raph manage to get the dinosaurs back into their rift and it closes.
Cut to New York City of the past, as Splinter and Don materialize in the middle of the street. They materialize right in front of a truck labeled TCRI and dodge the vehicle. Splinter immediately recognizes that they are back in the year 1990. Suddenly, a blind man walks into the street in front of the TCRI truck! The vehicle swerves to avoid the man as a boy pushes him out of the way. A canister on the back of the truck goes flying and bounces on the street - right at a little boy carrying four baby turtles in an aquarium! The canister hits the tank, shattering it. The turtles and canister fall into a storm drain, where the container breaks open and douses the reptiles with ooze! Splinter and Don have just witnessed their own mutant creation!
Cut to New York, year 2000. A rift opens and Leo and Cody fall out. As they look around, Leo realizes where exactly they are: it’s the Turtles' first battle with the Foot Clan!
Act 3: The Foot attack - Leo protects Cody and defeats them. Just then, Shredder appears!
Cut to Mikey and Raph as another rift opens in front of them. This window contains future versions of themselves! They’re in Sh’Okanabo’s ship, fighting Foot ninjas. As Raph and Mikey watch on, their future selves yell for them to get back to Cody’s penthouse, where there’s a piece of mail that can help. As the rift shuts, another opens releasing angry Vikings.
Cut back to Don and Splinter in 1990. Don realizes there’s only one way to fix everything, and it’s to turn Cody’s Time Window into a temporal beacon that can focus on their arm gauntlets and lead them home. With that, he draws up some schematics and puts them in an envelope to deliver to the post office.
Cut to Raph and Mikey as they arrive at the penthouse. They grab the letter from Serling (that's now 115 years old), and read - it's the plans that we just saw Donatello drawing up in the past!
Cut back to Cody and Leo in the year 2000. As the Shredder attacks, Cody can do nothing but watch on as Leo battles his foe.
Cut to Raph, Mikey and Serling as they work on the time machine. They finish their work and activate the Time Window - but it fails to function. Raph gets frustrated and kicks the machine - which causes it to start working!
Cut back to Don and Splinter in the year 1990 just after Don has finished mailing the missive. Splinter asks his son when they can expect to be rescued, and Donatello states that if everything went as planned - it should be right about now. On cue, the alley is bathed in bright light as a time rift appears.
Cut to Cody and Leo in the year 2000. Leo continues his skirmish with Shredder until a time rift opens behind him. Leonardo yells to Cody to run and they both escape through the portal.
Cut back to Cody’s lab where Splinter, Don, Leo and Cody materialize through the Time Window. The temporal beacon worked, but time and space are still collapsing! Our heroes must find the source of the problem, which Cody deciphers is located within the Chelsea Chasm.
Cut to Sh’Okanabo’s ship as the Hovershell pulls up. The Turtles, Splinter, and Cody find Sh’Okanabo and Viral in a panic, not knowing what to do. Cody offers to fix things when more rifts open inside the spacecraft. Out of the windows comes the Shredder and his crew of Foot ninjas!
Act 4: As the Foot attack, Cody and Don rush to the machine to make repairs. Sh’Okanabo helps the other Turtles fend off the Foot. Suddenly another rift opens, showing Raph and Mikey from earlier on. With that, the present Raph and Mikey remember that they must tell their past selves to go get the package. Once that is accomplished, the Turtles and Splinter, with Sh'Okanabo's help, finish off Shredder and the Foot, sending them back into their rifts.
With the enemies gone, Cody and Don finish fixing the Time Window and it stabilizes. All of the rifts are sucked back into the machine, save for one final rift that remains open. It’s a portal back to 2005! The Turtles and Splinter see their path home and move towards it as Cody says goodbye.
Sh’Okanabo, no longer in need of help, closes in on Cody.
The Turtles leap in to intervene! The heroes realized that they couldn't leave Cody in the evil alien's hands, so they did not enter the time rift before it sealed. Mike grabs Cody and pulls him away. Raph throws one of his sais and destroys the enemy's time machine. With that, the guys escape from the exploding craft and take off in the Hovershell, leaving a defeated Sh’Okanabo with nothing.
Later at Cody’s penthouse, the Turtles, Splinter and Cody can finally rest. Cody finds out from Officer Biggles that Chelsea Chasm is now empty, which means Sh’Okanabo is gone. The troubling question is how he obtained the plans for the Time Window in the first place...