Two years after their battle with Shredder and Eric Sacks, the Teenage Mutant Ninja Turtles, Leonardo, Donatello, Raphael, and Michelangelo, still live beneath the sewers of New York City, having allowed Vern Fenwick to take the credit for Shredder’s defeat. At Grand Central Station, April O’Neil discovers and informs the turtles that scientist Baxter Stockman is working for Shredder and plans to bust him out of prison. As Shredder is transferred between prisons alongside criminals Bebop and Rocksteady by corrections officer Casey Jones, the Foot Clan attack the convoy transporting them. Despite the turtles’ interference, Shredder escapes when Stockman uses a teleportation device. Shredder is hijacked mid-teleport, winds up in another dimension, and meets the alien warlord Krang, who reveals his plans to invade Earth. He gives Shredder a purple mutagenic compound in exchange for his promise to find three components of a machine that Krang sent to Earth long ago which will open a portal to his dimension when united, knowing that Shredder and Stockman have the first piece. Casey tells NYPD chief Rebecca Vincent what happened to Shredder but is met with disbelief, and decides to go out on his own. Shredder returns to NY, recruits Bebop and Rocksteady, who also escaped, and has Stockman use Krang’s mutagen to transform them into powerful animal mutants—a humanoid warthog and rhinoceros. April witnesses their transformation and is able to steal the remaining mutagen vial. Pursued by the Foot, she is rescued by Casey, who uses hockey gear, but the vial is taken into police custody. April then introduces Casey to the turtles, and Raphael and Michelangelo make fun of and pull pranks on him. In the lair, Donatello deduces that the mutagen could be used to turn the turtles into humans, enabling them to live normal lives above ground, but Leonardo refuses and insists on keeping it a secret from the others. However, Michelangelo overhears their conversation and tells Raphael, which enrages Raphael and leads to a fierce argument between the brothers. Leonardo benches Raphael and takes Michelangelo off the mission. In the Natural History Museum, Shredder, Bebop, and Rocksteady find the second piece and steal it before Leonardo and Donatello arrive. Still furious, Raphael recruits Michelangelo, April, Casey, and Vern to break into the NYPD headquarters and retrieve the mutagen. Vern distracts the police while April and Casey retrieve the mutagen, but the Foot arrive ahead of them. In the ensuing battle, the turtles’ existence is revealed to the police, who react with fear and hatred, and April and Casey are arrested while helping the brothers escape with the mutagen. Vincent also sees on TCRI’s cameras that April stole the mutagen, but Stockman had edited the tape so only April is seen. The turtles track Bebop and Rocksteady as they recover the final piece of the device in the rainforests of Manaus, Brazil, and board Rocksteady and Bebop’s jet in midair. In the resulting battle, the jet is critically damaged after Rocksteady fires a tank-mounted machine gun in the cargo hold, and crashes into a river. As the Turtles fight Bebop in the river for control of the piece, Rocksteady emerges in the tank and helps Bebop escape with the piece. The turtles return to NY as Shredder and Stockman complete the device and open a portal to Krang’s dimension through which his modular war machine, the Technodrome, begins to emerge. Shredder betrays Stockman and his men take him to their headquarters in Tokyo. When entering the Technodrome, Krang likewise betrays Shredder, freezing him and locking him with his collection of other defeated foes. Seeing no way to reach the Technodrome as the police pursue them, the turtles debate over taking the mutagen to become human and fight openly. While Leonardo agrees, Raphael shatters the vial, realizing they must accept who they are. Upon April’s request, Vern recovers the security footage from a hidden TCRI camera disguised as a clock that proves Stockman and Shredder’s collaboration and secures April and Casey’s release. April arranges a meeting between the turtles and Vincent, and convinces her that they are not enemies and were the ones who defeated Shredder in the first place. With the help of the police, the turtles are able to jump from the Chrysler Building and confront Krang aboard the still-assembling Technodrome. Although Krang is able to overpower all four turtles easily, they defeat him when Donatello short circuits Krang’s robotics body. April, Casey and Vern raid the Foot Clan facility, defeat Bebop, Rocksteady and Shredder’s lieutenant Karai and take control of the device. The turtles are able to hurl the ship’s beacon back through the portal, taking Krang and the rest of the Technodrome with it, as April, Casey, and Vern shut the portal down. As he disappears, Krang vows to return stronger for revenge. A week later, Bebop and Rocksteady are back in custody, while Stockman remains at large. At night, the turtles are honored by Vincent and the NYPD along with April, Casey, and Vern, and given golden keys to the city. Vincent offers to introduce the turtles to the public, allowing them to lead normal lives, but the turtles opt to keep their existence a secret while still helping as they always have. On top of the Statue of Liberty, the Teenage Mutant Ninja Turtles celebrate their victory over the vanquished Krang.