When the Time Window is finally repaired, the Turtles enter into it to head home, but instead of finding themselves back in the lair, our heroes find themselves with Viral! She’s escaped from inside Serling and has infected the Window so that she can send her most hated enemies on a harrowing, helter-skelter trip through the past, present and future and make them pay for all the pain they’ve caused her!
When the Turtles are reunited with Casey and April, it's smiles all around ... until it becomes clear that Casey's being brainwashed by his new martial arts instructor, Master Khan, a devoted Foot operative. The Turtles must save Casey (and themselves) from this deadly Foot fanatic.
The Turtles journey into cyberspace as Cybernauts on a mission to save as much of Master Splinter as they can find. But, they find far more than they bargined for as an old foe is re-born in the digital world...
Casey and Raph head to Chinatown to find an engagement ring for April. They find one, all right. Too bad it has dark, transformational powers. Powers that are of interest to Hun and the Purple Dragons as well.
While Don focuses on collecting Splinter’s data bits, his brothers find themselves pulled into a war between The Foot and the Purple Dragons. But things get a lot worse when the cyber-Shredder finds a way out of the digital realm by taking over the powerful robotic body of his old crony, Baxter Stockman! With Splinter’s data bits just within his grasp, Don is forced to make a terrible choice, help his father or help save his brothers from the Shredder.
Serling, desperate to return to his own time, builds a makeshift Time Window. Unfortunately, he accidentally shrinks himself to five inches tall and goes on a time traveling adventure. Unfortunately, when he escapes the clutches of arguing Turtles, he is found by Wendell, an old man who has been hunting him since Serling destroyed his toy eighty years previously and wants to reproduce him.
Cyber Shredder releases a virus that wipes out the Turtles' memories and brainwashes them into thinking they are his loyal Foot minions.
The Cyber Shredder creates a web portal that he hopes will allow him to venture from cyberspace into the real world. The villain first tests the device by releasing all sorts of mutants and monsters from various online programs. The Turtles must take down the creatures before they tear the city apart… and shut down the web portal before Cyber Shredder is able to use it and enter into the real world!
The Turtles find more of Splinter's data bits embedded within Mikey's favorite online video game superquest and have to play the game to retrieve them from the treasure.
Shredder makes the turtles believe they have left cyberspace, when they are really still there giving him important information about how to build a portal.
The Shredder hacks into a computer grid reprograms every electronic device in N.Y.
When Raph gets hold of a cape that grants him super powers, an impressed Justice Force invites him into their ranks and Mikey gets super jealous. But when Dr. Malignus tries to get the cape for his own villainous designs, Mikey and Raph must put aside their differences to save the city!
The Turtles and Master Splinter get ready for April and Casey's wedding.