One year after their confrontation with Shredder, the Teenage Mutant Ninja Turtles—Leonardo (the leader), Donatello (the brains), Raphael (the muscle), and Michelangelo (the pizza lover)—continue to dwell beneath the sewers. They’ve allowed Vern Fenwick (Will Arnett) to take credit for their victory over Shredder ([Brian Tee]), a decision that weighs heavily on their conscience.
Meanwhile, April O'Neil (Megan Fox) uncovers that a scientist named Baxter Stockman ([Tyler Perry]) is collaborating with Shredder, plotting to facilitate his escape from prison. Determined to thwart their scheme, April alerts the turtles. As Shredder is being transferred between prisons with two new criminals, Bebop and Rocksteady, brought in by Casey Jones ([Stephen Amell]), the Foot Clan launches a daring attack on the convoy. Despite the turtles' efforts, Shredder manages to escape when Stockman activates a teleportation device, though his escape goes awry, leaving him stranded in another dimension where he encounters the alien warlord, Krang.
Krang reveals his ambitious plans to invade Earth and more importantly, requests Shredder to retrieve three important components for a machine he sent to Earth long ago. In exchange, he grants him a mutagenic substance to eliminate the turtles. At the NYPD, Casey attempts to report the chaos to his chief, but does not gain any credibility. Choosing to take matters into his own hands, Casey decides to investigate further.
Back in New York City, Shredder returns and enlists Bebop and Rocksteady, who also managed to escape. With Stockman's help, they undergo terrifying transformations into powerful animal mutants—a warthog and a rhinoceros, respectively. Witnessing this transformation, April seizes the opportunity to steal a vial of mutagen but finds herself pursued by the Foot Clan. Luckily, she is rescued by Casey, who cleverly employs his hockey gear during the fray. What follows is a chaotic battle leading to the mutagen's temporary capture.
April gradually introduces Casey to the turtles, where hilarity ensues as Raphael and Michelangelo engage in playful teasing and pranks. Down in their lair, Donatello hypothesizes that the mutagen can convert the turtles into humans, granting them the chance to lead normal lives above ground. However, Leonardo is resistant and insists on keeping this secret from the rest. Discontent brews when Michelangelo eavesdrops and informs Raphael, igniting a fierce sibling clash. Leonardo takes drastic measures, sidelining Raphael and excluding Michelangelo from upcoming missions.
Meanwhile, at the National Museum of New York, Shredder and his henchmen successfully retrieve the second piece of Krang's machine just before Leonardo and Donatello could intervene. Fueled by rage, Raphael takes charge, enlisting Michelangelo, April, Casey, and Vern to infiltrate the NYPD headquarters and reclaim the mutagen. In this adrenaline-fueled escapade, the turtles' identities are revealed, triggering a mix of fear and disdain from the police. April and Casey rush to help the turtles escape, but they find themselves arrested as a consequence.
With Shredder’s forces recovering two components of the device, the turtles pursue Bebop and Rocksteady to the rainforests of Manaus, Brazil, where they attempt to seize the final piece. The battle in the air leads to a jet crash, but ultimately, Bebop and Rocksteady manage to escape with the last piece. Returning to New York, Shredder and Stockman are busy assembling a portal to Krang’s realm, causing chaos as Krang's dreadful Technodrome starts to emerge. Shredder's treachery unravels, as he gets betrayed by Krang, locking him away along with others from his past.
As the police hunt them down, the turtles contemplate using the mutagen to become human and confront Krang. With both sides debating the issue, Raphael counters Leonardo's decision to take the mutagen, enlightening them that they should embrace their true selves instead. April convinces Vern to obtain crucial security footage that exonerates April and Casey, paving the way for a meeting with Police Chief Rebecca Vincent. Fortunately, they manage to earn the police's trust, revealing that they were responsible for the downfall of Shredder.
With the NYPD's aid, the turtles charge into battle against Krang on the still-constructing Technodrome. Though Krang showcases his immense power, it’s Donatello who ultimately short circuits Krang's robotic body, leading to their triumph. Meanwhile, Casey cleverly handles Bebop and Rocksteady, trapping them in a grenade-filled crate, while April takes on Shredder's lieutenant, Karai. Together, they successfully hurl the beacon back through the portal, sending Krang and the Technodrome back to his dimension.
In the aftermath, Bebop and Rocksteady are recaptured, but Stockman remains at large. As the city lights shimmer at night, the turtles are honored by Vincent and the NYPD alongside April, Casey, and Vern, who present them with golden keys to the city. Though they've been offered a chance to reveal their existence, the turtles decide to keep their identities a secret, knowing that they will always have allies when in need. As they stand atop the Statue of Liberty, the Teenage Mutant Ninja Turtles celebrate their hard-earned victory over Krang, pledging to continue their watch over the city.
