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With the Technodrome in serious need for new equipment, Bebop and Rocksteady are sent to Earth, disguised in human form, to capture the Channel 6 building and take it to Dimension X. To keep the Turtles distracted, Rocksteady & Bebop also deploy a robot duplicate of Master Splinter, but it malfunctions and starts going gonzo.

Vengeful Baxter Stockman and an A.I. computer return to Earth from a dimensional limbo and capture the Turtles while luring Shredder into their trap as well.

Note: As in the third season in the series Bye, Bye, Fly

On their latest trip to Earth, Bebop and Rocksteady steal a machine that makes everyone scared of everything.

When General Tragg and his troops attack the Neutrino planet capital, the Neutrino leaders, King Zenter and Queen Gizzla, send their infant daughter Tribble through a portal to Earth, asking the Turtles to look after her, but Tribble causes big trouble for our heroes.

An eccentric billionaire, Monroe Q. Flem, who is also a collector, wishes to collect every piece of TMNT memorabilia that he can get his evil hands on, including April O'Neil and the Turtles themselves.

Raphael must contend with a mobster named Pinky McFingers when he is kidnapped from a local comedy club. (This is the only episode appearance of Baxter Stockman's twin brother Barney Stockman.)

Bebop and Rocksteady use Krang's new Mutagen on Bebop's pet turtle Slash so he can do their housework for them. Slash runs away and is conned by an irritated entrepreneur into framing the TMNT. Note: First Appearance of Slash and Donald J. Lofty.

Note: Donald J. Lofty will return in the series The Big Zipp Attack

Krang hires a multi-dimensional ring-master who intends on making the Teenage Mutant Ninja Turtles part of his circus by using an anti-aging serum. Leonardo and Michaelangelo are turned into 5 Year olds.

When Michaelangelo decides to put one of Donatello's inventions on max power for his own entertainment, he ends in a—quite literally—little problem. April and Vernon get caught in the shrinking ray while getting footage of a military ship and join Michaelangelo on his wild adventure.

An alien called a "Zipp" is sent to Earth, but this little alien soon becomes a big problem.

Note: Donald J. Lofty as in the first appearance in the series Slash – The Evil Turtle from Dimension X

Dr. Polidorius, a mad scientist plotting to mutate all humanity into aquatic-beings, creates Ray (not the similarly-named Mighty Mutanimals character), who possesses several abilities of different marine species. Ray kidnaps April O'Neil, and Polidorius mutates her into a fish-woman to be Ray's mate.

Note: Donald J. Lofty As in the series Slash – The Evil Turtle from Dimension X and The Big Zipp Attack

Michaelangelo meets his favourite comic book hero after he saves a weakened Brick Bradley in the sewers, and then he and Bugman take on the evil Electrozapper together.

The Turtles must baby-sit and protect a young rich girl named Buffy Shellhammer from Shredder and Krang, as she knows of a formula for a super fuel needed for the Technodrome.

Shredder has a plan to destroy the Turtles, but with the Technodrome's portal out of commission, he is unable to challenge them on Earth, so he uses the Dimensional Teleporter to bring his enemies to Dimension X.

Donatello earns his degree from Sopho University, but discovers that he has been mistaken for a girl, so he asks Irma to masquerade as him. Meanwhile, the real Donatello discovers a plot by Professor Philo Sopho to destroy the Earth.

The Turtles switch sides and discover that the Shredder is the main man behind a ring of cufflink thefts that has suddenly hit New York City.

Leonardo becomes addicted to a new arcade game, Tempestra's Revenge, which ends up affecting his usual routine. But when a freak power surge releases Tempestra from the cabinet, Leonardo has to stop her digital wrath before she becomes dangerously powerful.

Gadget Man comes out of retirement after 50 years, but is tricked by Shredder into fighting against the Turtles.

Set up as a follow-up episode, Hokum Hare and the Turtles hitch a ride on a time-traveling train to 2036, where they discover that Shredder has plans for the future New York City. Ultimately, the Turtles of both the past and the future must team up to thwart Shredder before his actions cause all of time to be destroyed. Title Reference: Once upon a time

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