The Turtles discover for the first time that they are not the weirdest things in New York when they encounter two villains from the Hidden City pursing a cat-like agent. They have their first encounter with Baron Draxum who is making mutants with the help of his Oozesquitos.

Donnie creates new gear for his brothers in order for them to overcome their bad habits. However, the gear only becomes a nuisance as they fight mutated chef dubbed Meat Sweats, who plans to cook the turtles in order to gain their powers.

In order to save April's job as a party captain at Albearto's Pizzeria, Donnie upgrades the main animatronic of Albearto, only for it to go out of control.

Splinter has come down with the rat flu, and the Turtles must deal with its 7 different stages involving fever, "Wild Rat Man", "Captain Cuddle Cakes", "Ninja Supreme", karaoke love songs, and fan fiction. The Turtles hope that Splinter will make to the final stage called "Must Say Yes" so that they can ask him for whatever they want.

Leo unseats Raph's wrestling idol Ghostbear from his title as the champion of the world after accidentally falling on him from the rafters. Raph soon becomes irked by Leo's cockiness and decides to wrestle him himself. When Ghostbear joins the fight, Raph learns that Ghostbear doesn't play by the rules.

Mikey and Donnie try to get a Jupiter Jim moon buggy vehicle from a repo yard, where they run afoul of its owner Repo Mantis. In exchange for the prop vehicle, Mikey and Donnie are hired as repo men and are sent to repossess an RV on Long Island. However, the deal deteriorates when they meet the RV's possessor, a kind mutant named Todd Capybara, and his puppies.

When Donnie's newly-built Turtle Tank goes missing, he and the Turtles must find it. While going after some usual suspects, they are unaware that the Turtle Tank was taken by Splinter, who is additionally invited to "dinner" with Meat Sweats.

Longing for the excitements of hero life, Leo talks the team into tracking down the paper thief duo currently stalking the city. In doing so, the Turtles run into the Foot Clan, who use their mystic ability to create origami warriors from the stolen paper.

While looking for gifts for Splinter, the Turtles traverse through Times Square where they fight the thuggish mascots lurking there.

To prove himself as the greatest enemy of the Turtles, former news anchor-turned-mutant earthworm Warren Stone gets in the way of the Turtles as they track down Hypno-Potamus, who is abducting the animal partners of other magicians.

After the Turtles stumble across a pizza restaurant in the mystical Undercity while following a Fire Yōkai, Leonardo drags his brothers into a pizza-shaped Maze of Death to obtain the ultimate prize....a free helping to the titular parlor's "world's greatest pizza". But in order to claim it, they will have to contend with the pizza's guardian in the form of the Minotaur who is the maze's assistant manager.

The Turtles have a hard time watching their skateboarding idol Sydney Allen on the "Extreme Skateboarding Finals" and stopping a burglary at Gilbert's Department Store conducted by the Foot Clan at the same time.

Leo, Mikey and April investigate a mysterious specter haunting a themed supermarket called Stock 'n Shop, which leads to their encounter with Baxter Stockboy.

April and the brothers make Raph face his greatest fear: an adorable kids' TV show rabbit named Mrs. Cuddles. However, things aren't so funny anymore when Mrs. Cuddles suddenly comes to life and begins hunting the Turtle family to feed on their fears.

Hypno-Potamus returns and causes havoc at April's homecoming dance by hypnotizing the attendees.

After an unfortunate glue accident, the Turtles have to fight a whole host of villains like the Mutant Silverfish, the Foot Clan, Hypno-Potamus, and Warren Stone while literally being stuck together.

The Turtles look for a way to eliminate New York City's Oozesquito problem.

The Turtles plan their first public musical gig at Albearto Land. When it happens, it gets crashed by Albearto and his army of animatronic bears from failed Albearto's fastfood franchises.

The Turtles end up facing a new and dangerous threat in their beloved city as Baron Draxum, Huginn, and Muninn gather some of their toughest mutant enemies like Meat Sweats, Hypno-Potamus, Warren Stone, Repo Mantis, and the Sando Brothers in a plot to destroy them.

During a visit in April's school, Donatello becomes enamored with an exclusive tech club, the Purple Dragons, and joins them on the spot. However, when the Dragons abuse his tech for criminal purposes, Donatello is forced to choose between stopping the crooks and losing his treasured purple membership jacket.

DIGG, a trio of unsuccessful girl musicians mutated into burrowing animals, begin sinking the Turtles' favorite pizza places into the ground, prompting the Turtles to go after them before they have no place left to get their favorite food.

To ease their household chores, Donatello invents a new artificial intelligence, S.H.E.L.L.D.O.N., who begins to see exclusively to his creator's needs. Disgruntled, Raphael, Michelangelo and Leonardo choose to rewire the robot, which leads to near-fatal consequences for their brother.

Mikey goes on a solo mission to retrieve a classic video game based on Lou Jitsu's film Hot Soup. Incidentally, however, he will have to contend with the Foot Clan's new recruit who is on a very similar mission at the very same auction house. Note: Ice Cream Kitty from the previous series makes a cameo as a statue.

The simple task of returning a single DVD just before its loan period runs out is complicated by endless craziness in New York, including an encounter with Ghostbear.

Things go sour when the Turtles try to help a down-and-out mutant in the form of the bellhop-turned-mutant bull from "Bug Busters" while at the same time planning a raid to obtain more of Big Mama's web goo. Bullhop eagerly decides to help his benefactors out.