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 pursuing 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 at Albearto's, 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.
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 and their mystic ability to create origami warriors.
While looking for a new robe for Splinter, the Turtles traverse through Times Square, where they fight the mascots lurking there who get jealous of Raphael's "Turtlepotamus" meme. When they take the money that Raphael has made, the other Turtles suit up and take action against the mascot - until they discover the true identity of the mascots as mutant cockroaches.
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.