Cynthia Utrom, the executive of the Techno Cosmic Research Institute (TCRI), sends a team to track down rogue scientist Baxter Stockman. He's developed a mutagenic ooze with ambitions of crafting his own mutant animal family, starting with a housefly. During the hunt, however, his plans unravel in a chaotic explosion, resulting in his demise and leaving the mutagen to seep into the sewers of New York City. The lone mutant housefly manages to escape.
As the mutagen spreads, it transforms four turtle brothers—Michelangelo, Leonardo (Nicolas Cantu), Raphael (Brady Noon), and Donatello (Micah Abbey)—along with a rat named Splinter, into humanoid mutants. Embracing their new forms, Splinter, filled with caution from past experiences, insists that the turtles must stay hidden from humans, particularly after a troubling encounter at Times Square where they were chased away. He trains his sons in the art of Ninjutsu and maintains that their excursions should be limited to stealing supplies.
The years pass as the turtles yearn for acceptance in human society, much to Splinter's discontent. He has instilled within them the belief that they, as mutants, would never be embraced by humanity. However, their desire to experience life like human teenagers grows stronger. Leonardo, the de facto leader, faces challenges as his brothers often disregard his warnings to remain cautious.
Fifteen years fly by, and while practicing their Ninjutsu skills on a rooftop, they inadvertently injure a girl on the street with a ninja star. Fortunately, she is only wearing a helmet, but as tensions rise, her scooter is stolen. This incident propels the turtles into action; they pursue the scooter to a warehouse, dismantling a criminal gang and retrieving a moped owned by a teenager named April O'Neil. This marks their first real fight, fueling their confidence.
When they share their story with April, she’s captivated and reveals her aspirations as a journalist striving to overcome a viral moment where she vomited on camera. April has been investigating a string of thefts involving TCRI tech orchestrated by a criminal named Superfly. She believes that by writing about the turtles, she can shift public perception in their favor.
In response to the thefts, Cynthia implements tracking devices on her tech. Driven by a newfound purpose, the turtles plan to thwart Superfly’s operations and utilize April’s journalism to gain acceptance as heroes. They begin by confronting henchmen assisting in the thefts. After intercepting a stolen device, they meet Superfly, who reveals himself not only as a mutant but also as the leader of a gang that includes Rocksteady, Bebop, Wingnut, Leatherhead (Rose Byrne), Mondo Gecko, and others. Thrilled to connect with fellow mutants, the turtles bond over their shared experiences and learn about their origins tied to Stockman.
Superfly divulges his elaborate scheme—to use the stolen technology to mutate all animals on Earth to declare mutant supremacy over humans. In a sinister twist, he plans to weaponize the mutagen and release it into the atmosphere, turning humans into pets. Attempting to avert catastrophe, the turtles confront him, but their efforts backfire as they get captured instead. At TCRI headquarters, Cynthia begins extracting their mutagen for her ambitious plan of creating super soldiers with hybrid features.
But just in time, April and Splinter embark on a rescue mission. The stakes are high, as Splinter and the turtles rush to thwart Superfly's machinery. They engage in a critical dialogue that shifts perspective, persuading the gang that descending to humanity’s worst traits would ultimately tarnish their stature as mutants. United, they dismantle the machine, albeit with repercussions—the ooze spills into the water, mutating Superfly into a massive whale-like kaiju that wreaks havoc in the city.
The turtles, now misperceived as further monsters, rally together to stop him. Leonardo steps into his role as the leader, while April pushes through her anxiety to commandeer a news broadcast, clarifying their intentions and garnering the city’s support. In a heroic display, the turtles, with assistance from the mutants and citizens, manage to neutralize Superfly by employing TCRI’s retro-mutagen.
In the aftermath, harmony prevails as the turtles are celebrated by the city, greeted as heroes. The mutants move into their sewer home, and romantic sparks fly between Splinter and Scumbug. The turtles begin attending April's high school, finding acceptance and cheering camaraderie. As they celebrate at prom, they remain unaware of Cynthia’s watchful gaze, plotting with the enigmatic Shredder to reclaim the turtles.
