We travel dark New York streets, a tour of crime and violence and despair. A voiceover, split between the four turtles, summarizes the situation:

With The Shredder dead, the city should have been saved, but crime runs rampant. The Foot, without a leader, without a plan, terrorize New York. From the resulting chaos, dozens of blood-thirsty gangs have emerged, all fighting for territory, all killing for the same scraps. Criminal organizations that once ruled the city from the shadows have taken to the streets to protect their corners of a world in decay. The NYPD, the only soldiers capable of restoring order, stand divided. One half fights for justice, desperately hoping to keep citizens safe. The other is in league with the criminals. Officially, to those still concerned with the law, we are vigilantes. To the gangs and crime lords we are a nuisance. To the people bold enough to believe the whispers, we are monsters. To us, we’re a lot of things: ninjas, brothers, New Yorkers, turtles, and with half a chance and an ally or two, we can become what this city truly needs. Heroes.

The camera stops on three of the turtles perched above a warehouse on the docks. Leonardo points out the guard at the adjacent warehouse. Donatello checks a handheld device and sees a blip moving in from the west. He tells the others the Foot is almost here and the police should arrive in about 15 minutes. With the right timing, they’ll catch Shredder’s former clan in the act of stealing mafia-stolen goods and two criminal groups will take a simultaneous hit. Michelangelo complains that the turtles won’t be directly involved, but Donatello defends this sidelines approach.

As if on cue, a small group of thugs dressed in wild costumes appears, one wearing a giant foam clown head. The band attacks the guard and sneak inside the warehouse. It’s a stealth invasion with no sound of guns, but a moment later two vans pull up and a dozen thugs jump out in bulletproof vests and riot helmets. Leo asks if it’s the cops and Donny says no. They must be wearing stolen police gear. His point is proven when they kill the foot clan guard and rush inside the warehouse. It looks like this gang is a rival to the Foot and they don’t operate quietly. From inside, even more gunshots ring out.

The turtles are unsure of what to do. The real police should be there soon to foil the triple gang war, but people are dying inside. The turtles decide to intervene and make their way to the warehouse. Inside they see pinned down mafia and foot clan members, dead from each lining the aisles of the warehouse. The turtle trio begin to fight all three groups, hoping to keep the death toll from rising until the cops get on scene, but the cops never show. The Foot and the rival gang make decent foes, but when the Foot suddenly leave, the other gang disperses and flees. The only people left are three Italian men, one of them the head mafia boss.

He’s not weirded out by the appearance of the turtles. If anything, he’s fascinated, but he doesn’t know if his men should fight or give thanks for running the other gangs off. He complains about what the city has become, nostalgic for the order and civility of the past, when crime had class. Now he’s scared for his kids, and happy to know the turtles are real, a group that might actually do some good in a city where the cops are more corrupt than those they put in prison. He’s interrupted by one of his men shouting about a bomb. Before he can finish his warning, the bomb explodes and everyone cowers. Leonardo pulls the mob boss in close and the blast is shielded by Leo’s shell as it is with the other turtles. They fight through flaming debris to get to safety, choking on black smoke. The only survivors are the turtles and the mob boss. This time he knows a thank you is in order. Sirens are finally heard in the distance and the turtles decide to disappear.

Back at turtles HQ, the Leo, Mikey, and Donnie are settling in when the Foot clan clown enters. He removes his mask to reveal Raphael beneath. He has infiltrated The Foot in an attempt to gather info while steering the organization toward less violent methods. The info he gathers goes to Donnie who now has an anonymous connection inside the police. While the crew discuss what went down at the warehouses he reaches out to his contact. The faceless cop tells him he ran into problems getting the police to act on his tips given the state of the city. It’s hard to send cops out to a possible crime when active crimes are always in the works, but he’s trying.

Leo argues that they can’t rely on anyone else to help them. Donnie defends needing the cops as allies. Raph says he believes the Foot are the key to taking down the other gangs and the corrupt cops, dismantling them entirely when the job is done. They don’t know who the other gang was other than a dragon symbol on the vans, but they’re not surprised that yet another gang has sprung up. Mikey sits back eating pizza. Splinter tells them allies are important, but trust and control are strongest with a core group.

We cut to the cop just finishing his communication with Donnie. His badge says Williamson. He looks stressed and there’s a frantic bustling in the police station around him. The cops are talking about the warehouse too and the general state of the city. Williamson walks through several groups of chatter, some calling for more staff, others saying it’s too late. He makes his way out of the police station to the impound where a couple of vans are parked, each decorated with a dragon emblem. He opens one up to show a bag in the cargo area. Inside the bag are explosives and cell phones. He grabs a phone, closes everything up, and leaves.

From here we cut to Raph in his clown costume. He is training with a Foot clan sensei, Aoki, one of the last upper-tier commanders of the Foot. They spar as equals then talk about what the Foot has become and where they are headed. Aoki says he was never interested in The Shredder’s master plans, but he knows the Foot can still have power. To become powerful again they must have great generals, leaders of small groups operating independently but under one name. Raph asks if The Foot can’t be something else besides criminals and Aoki says their greed and hate is far less than those in charge of the city. The Foot is merely unwilling to be citizens of a hypocritical government.

Aoki and Raph’s relationship strengthens, especially when Raph and Leo have a falling out about strategy. Aoki converts Raph into a new viewpoint and direction for the Foot, becoming vigilantes to sway governments over stealing stereos, but Raph won’t support murder and terrorism. Donnie continues feeding Raph’s info to Williamson on crimes planned by more violent factions of The Foot, meanwhile investigating the origin of the dragon vans. The mob boss strikes back at the Foot, shooting up their various hideouts. The turtles want to take them down and turn them into the cops, but Donnie discovers the vans belonged to an old gang that was shut down by the police years before when Shredder thinned their numbers. He tracks the vans back to the police impound and discovers cops have been using them at night for criminal enterprise. While he looks for new, more trustworthy cops, Leo goes to speak with the mob.

He negotiates a cease fire between the mob boss and Raph’s faction of the Foot, but Aoki strikes out against the mob boss. The turtles and mob fight the Foot while Raph takes on Aoki. Raph pins down his sensei and tells him murder was Shredder’s way. It doesn’t have to be theirs. Raph tells the mob boss he accepts their truce and he will do his best to keep the Foot in line as its new leader. After the meeting, the turtle brothers gather and confront Raph about his plan, but receive word that the Dragons are on the move en masse and they’re killing members of the Foot clan. Raph says the city will always have criminals, so they need the right kind of criminals to keep the violence down. He wants to remain the leader of the Foot and he’ll do whatever it takes to keep them at the top of the criminal food chain.

The three turtles go to chase down the Dragons and once again fight the Dragons and the Foot. One of the corrupt cops is killed by one of the violent Foot faction members and the Dragons run, but Donnie sees the police are pinning the murder on the turtles. All the police, corrupt or not, are on the hunt for the turtles. Raph pulls in all factions of the Foot to announce himself as its new boss. With Aoki’s support, the hundreds accept. Donnie finds out Raph’s Foot is planning to make a sweep of the city, scattering any gang that stands in their way.

Donnie sends the info off to Williamson and another file off to a list of additional NYPD. Everyone hits the streets of New York, the turtles, The Foot, and the Dragons and the turtles are forcing foot soldiers and Dragons into a common block, Raph and Williamson leading, but as the confrontation begins Raph and a select few of the Foot hang back and the turtles retreat to the shadows. Just as the remaining troops converge, NYPD show up sirens blaring. Williamson claims his men were under cover but one of the good cops shows him video Donnie sent proving Williamson’s criminal activities. The Dragons and most of the Foot are arrested.

The movie wraps up showing the turtles out fighting crime. Raph is training his new Foot. The mob boss is refilling his warehouse, and Donnie has a new connection with the NYPD, one sending him info as well. They gather at turtle HQ again where the dynamic is different, but the pizza is the same.