Battle alongside your brothers through the sewers, subways, and streets of NYC to take down Shredder and Krang's evil organization, Foot by Foot. Unleash custom combat skills and powerful team combos to save Manhattan from the overwhelming dark forces growing in the shadows.

At night atop the TCRI building Krang and Shredder meet on the skyscraper's helipad to confirm that everything is in place for their alliance towards an unspecified goal. At a gesture from Shredder, hundreds of Foot Clan soldiers descend upon the city, starting a titanic crime wave that throws the city into chaos. In their Lair deep beneath the streets, the Turtles discuss the crime wave with Splinter and April O'Neil, concluding that they are honor bound to protect the city and head out to do just that though Michelangelo is still in the middle of some pizza he feels similarly 'honor bound' to finish off.

While patrolling the rooftops, the Turtles notice Foot Soldiers sneaking around the Purple Dragons' territory and head to the streets to investigate the anomaly and clear out the rival ninjas. By preventing the Foot's crimes around the area, they gather enough intel for April to deduce Bebop is robbing the local bank and confront the mutant in the vault with devastating ninja moves and even worse piggy bank puns. Defeated, Bebop smashes a hole in the wall and escapes leaving behind his duffel bag full of stolen cash. Leonardo, Raphael, and Donatello wonder why Bebop would go to the trouble of robbing the place only to leave his loot behind. Mikey meanwhile is busy trying to take advantage of a stack of bills he sneaked, phoning for an order of a couple of thousand pizzas and bread sticks....an order he has to cancel because the other Turtles are clearly not amused.

Investigating disrupted subway activity the Turtles discover that a ton of damage has been done to the systems switch-boxes, shutting down entire lines and risking future collisions. The amount of rubble indicates possibly mutant based strength instead of simple ninja weapons. They discover a near by station already shut down and infested with not just Foot ninjas but also Rock Soldiers from Dimension X. After completing enough objectives they gain the intel needed to shut down a laser grid and advance into an active line, where they must contend with waves of Mousers as well as larger Rock Soldiers to shut down a series of bombs and a final laser grid before advancing to a confrontation with Rocksteady in an abandoned station. Though defeated, the rhino promises the Turtles that the havoc so far is "only the beginning", using an oncoming subway train to disappear into the shadows.