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.
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.
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
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.
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.
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.
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.
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.
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.
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 look for a way to eliminate New York City's Oozesquito problem before more mutants are made. This plot brings them into conflict with Big Mama in her plot to make mutants to fight for her entertainment in the Battle Nexus, which is soon joined by Baron Draxum.
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.
Hypno-Potamus returns and causes havoc at April's homecoming dance by hypnotizing the attendees.
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.
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 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.
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.
It’s Pizza Week, the greatest week of the year, but the Turtles’ favorite pizza joints keep getting taken out. 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.
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.
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 on the Grand Nexus Hotel to obtain more of Big Mama's web goo. Bullhop eagerly decides to help his benefactors out.
Frustrated by his brothers' childishness during an important mission, Donatello enhances their intelligence. However, things get quickly out of hand when they begin displaying Donatello's personality traits as well.
When Michelangelo and Todd Capybara spy on Meat Sweats in order to learn his most delicious recipe, the Turtle and the mutant chef become BFFs after Meat Sweats accidentally absorbs Todd's niceness. The two of them go on a look for the extremely rare lunar truffle that only grows when the Moon is in alignment with Jupiter, and face its Were-Tree guardian.
As the Turtles try to find pieces of a strange metal Baron Draxum is looking for, Splinter intents to get to the bottom of these odd activities at April's new job at the Foot Shack. He soon learns that the Foot plan to resurrect their ancient master the Shredder by reassembling the Kuroi Yoroi armor. As the parties clash, the secrets of Splinter's past finally come to light.
Leo loses his brothers in a portal and must venture to the mystic Hidden City to save them while dragging Señor Hueso along for the ride. He suspects that they are on the pirate ship run by Señor Hueso's brother Capitán Piel.
Baron Draxum, Huginn, and Muninn want the gauntlet that Warren Stone has since it's part of the Kuroi Yoroi armor, but he's not giving it up without a fight and a side of betrayal. As the Turtles get involved with Warren's roommate Hypno-Potamus being threatened, April remembers who Warren Stone is as she was part of a fan club dedidicated to him called the Stoneheads.
Leo and Donnie try desperately to help April enjoy a quiet day with a new friend named Sunita. They learn that she is a slime Yōkai who uses a special amulet to turn into a human. They soon get targeted by the Foot Clan since the boots that Sunita's human form is wearing are part of the Kuroi Yoroi.
Raph becomes friends with a new sparring partner in the form of Frankenfoot and must keep it secret from his brothers, who don't like the guy. When Frankenfoot is driven from the lair, this gives the Foot Lieutenant and the Foot Recruit the opportunity to take it into the Foot Clan.
Señor Hueso has just remembered that an ogre gang called the Makers of Brutality and a reptilian gang called the Makers of Barbarianism have book reservations at Run of the Mill Pizza. While helping Señor Hueso at Run of the Mill Pizza since his employees have fled, Leo and Mikey get sidetracked by brotherly competition. They must overcome this to keep the peace while trying not to wreck Run of the Mill Pizza.
Baron Draxum struggles to move up the ladder in the Foot Clan while Foot Recruit was displeased that she hasn't gotten her mark yet. Upon finding a loophole where a Foot Clan member who can outdo an acting leader can assume this position, Baron Draxum leads the Foot Recruit into organizing a blunder for the Foot Lieutenant and the Foot Brute when the next Kuroi Yoroi fragment is at the botanical gardens. Meanwhile, the Turtles hold a contest to see who can withstand the smell of the corpse flower at the same botanical gardens.
The Turtles plumb the depths of a mysterious hidden library in search of a way to rescue Mayhem from within April's mirror. While trying to be quiet, they must also evade not having a sound heard by the Bat Librarian's Hush-Bats and contend with the Foot Lieutenant and Foot Brute.
When a competitive new video game sweeps New York, Donnie will do anything to reach rank No. 1. Donnie is unaware, however, that the video game was created by the Purple Dragons as a way of getting revenge on him.
The TMNT's lazy river ride through the sewers turns savage when Raph is accidentally separated and left alone. This leads to him trying to survive the sewers and having an encounter with the Sando Brothers.
Baxter Stockboy begins revealing the Turtles' existence and turning public opinion against them in order to make some big money. The Turtles' failed attempts to clear their image turn all of New York against them.
Wanting to live with glory again, Splinter ropes Donatello and Michelangelo into modifying the Turtle Tank and entering it into a mutant demolition derby run by Big Mama. They face competition from Meat Sweats, Repo Mantis, Hypno-Potamus, and Warren Stone. It gets intense when Big Mama, the Fox Bellhop, the Otter Bellhop, and the Owl Bellhop get involved.
To prepare the Turtles for any future threats, Splinter teaches them some stealth training. After that is done, he sends them on a test to infiltrate the Grand Nexus Hotel to steal Gus's dog tags. When they appear to take too long, Splinter sneaks into the Grand Nexus Hotel, steals the Octopus Elevator Operator's outfit, and plans to find the Turtles before Gus, Big Mama, or the bellhops do.
Donatello and Michelangelo try to recover a piece of the Dark Armor from Repo Mantis' scrap yard that he claimed. Though they will have to contend with Repo Mantis first. Meanwhile, Raphael and Leonardo get impatient and check out a bus where they accidentally release Repo Mantis' pet cat Mrs. Nubbins.
The Turtles, April, and Mayhem are spending a snow day together. Meanwhile, Ghostbear has mutated into a mutant polar bear after coming in contact with an Oozesquito that Michelangelo defrosted. In this form, he uses his intangibilty in a plot to ruin April and the Turtles' fun day in the snow by targeting their snowman.
April and Sunita search New York for Sunita's stolen cloaking brooch after attending a DIGG concent. They find that it was stolen by Meat Sweats so that he can regain his human form and his hosting job on "Kondescending Kitchen" from a bound and gagged Guy Flambe. Meanwhile, Splinter's plan to take the Turtles on a wilderness survival training backfires when Raphael accidentally places the Turtle Tank on a 24-hour lockdown.
Having gotten bored of Splinter's Lou Jitsu stories, the Turtles head to a convention and meet Marcus Moncrief who portrays their favorite sci-fi movie character Jupiter Jim. When they go to his apartment, they find that he has started to see the different trapped fans as the aliens that Jupiter Jim fought in the movies and comics where Marcus has become more immersed in his character to the point he thinks he is actually Jupiter Jim.
With the help of Baron Draxum and the Guardsmen, the Foot Clan begin to move the nearly-completed Kuroi Yoroi armor to a ritual site. To transport it, Baron Draxum persuades Big Mama to lend the Foot Clan her train. After training the Turtles following the advice of his ancestors, Splinter trains the Turtles for this fight.
The Turtles have been captured, and Baron Draxum sends April back to have Splinter bring the final piece of the Kuroi Yoroi armor to him or else. As the faceplate is on his teapot, Splinter comes up with a plan to rescue his sons with the help of April, Bullhop, Frankenfoot, S.H.E.L.L.D.O.N, and Todd Capybara. When Baron Draxum reassembles the Kuroi Yoroi armor and dons it, the Turtles must find a way to get the Kuroi Yoroi armor off of him.
The TMNT must stop a persistent foe from shredding NYC, but problems arise when they split up to handle things.
The TMNT need to learn how to listen and get in touch with nature in order to save Todd after he's captured by a group of hunters.
Huginn and Muninn recall their first day working for Baron Draxum.
The Turtles have a secret that comes back to haunt them in the form of Splinter's pet goldfish Piebald who was accidentally flushed down the toilet and mutated after eating an Oozesquito.
April presents her award winning documentary about the Turtles’ at an annual event: The Lair Olympics. This year's event, however, takes a surprise turn when Donatello unexpectedly gains ground against the past games' constant champion, Leonardo, sparking a fierce competition between the two brothers.
Donnie's parenting causes S.H.E.L.L.D.O.N. to run away.
Mikey tries to get Draxum to tolerate humans.
Leo gets his dream job as mascot of the local professional basketball team.
Ralph teaches his brothers a lesson in responsibility.
With their favorite space hero movie star in need of a sidekick, the TMNT do all they can to win their dream job.
Leo and Senor Hueso help the reformed Capitan Piel on one last dangerous mission.
April and Splinter encounter a gang of dangerous middle school brownie sellers.
Baron Draxum's lunchroom concoction comes to life and terrorizes April's school.
Always a man of science, Donnie can't accept April going to the witches for mystic help on a science project.
Raph is mistaken for a heinous criminal in the Hidden City.
Leo's efforts to get into an exclusive Hidden City spa threaten to unweave his day of relaxation.
Splinter's magical day with Mikey is interrupted by a mysterious and tiny guest.
April and the Turtles must help Splinter save his chain of dojos from being taken over by an evil rival.
Hypno-Potamus traps the Turtles in a magical 80s movie montage.
Big Mama turns New York City into her new Battle Nexus arena and the TMNT have to fight to save everyone they love.
When a powerful foe returns, the Turtles' only hope lies within the most dangerous place they've ever been: Splinter's mind.
The Turtles meet Splinter's distant relative and discover a powerful new ally.
In a bid to save New York and the Hidden City, the Turtles prepare for their greatest battle yet.
When the Turtles find their ninpo, they must defeat the Shredder once and for all.
The young brothers play with their original weapons.
