as baxter stockman is transported to tokyo, tcri scientists take down the foot soldiers. one of them is the boss of tcri Cynthia utrom. they turn around and head back to the city. bat at manhatten, two crooks named groundchuck and dirtbag hyjack a truck and drive down the street. however, they are t boned by the tataruga brothers van with the turtles. vincent and casey arrive at the scene to arrest them while the turtles flee to the sewer. they return to splinter who is watching april o neils report on tcri. mikey is starting to wish that the public knew about them. after the report, april speaks with vernon, who is still living the dream.
at tcri, baxter wants revenge on the foot clan, that is under the command of karai after shredder was frozen. they want to target foot clan propertys, but have nobody to do it since bebop and rocksteady work for the foot and are in prison. utrom decides to break groundchuck and dirtbag out of a prison transport van. the two are taken to tcri. april sneaks in to see whatnthere plan is and takes vernon with her. they use mutagen from krang to turn them into a bull and mole.april and vernon destroy all the other ooze leaving one canister left. groundchuck and dirtbag go after them but they escape.
meanwhile,mikey asks vincent on behalf of the turtles to reveal them. vincent does and there are mixed reactiojs. some people like the turtles while others hate them and treat them like monsters. the turtles get angry at mikey, who is upset that there is so much hate to them there is a mutant murder cult. mikey already regrets the decision. at a foot clan warehouse, groundchuck and dirtbag do their first mission. this arrises the attention of karai who plans on attacking tcri. the turtles arrive at the scene and find holes underground and destruction witch could only happen from mutants.april tells the turtles of baxters plan after being apologised to by bernadette Thompson who thought she was crasy. the turtles track another foot warehouse where karai becomes prepared for groundchuck and dirtbag. a fight breaks out between them all witch ends with the turtles retreating and karai following groundchuck and dirtbag.
the turtles problems become worse when the cult finds there lair causing them to move out and find a new lair. after finding a new lair, the turtles head to tcri to finish this. at tcri, karai and the foot battle baxter,cyntia,groundchuck and dirtbag while the turtles arrive.the police arrive making everyone to escape accept for baxter who is arrested by casey and the turtles. cynthia sends groundchuck and dirtbag to break baxter out. the turtles,april,vernon and casey arrive and the two mutants release everyone from their cells, including bebop,rocksteady and erick sacks. bebop and rocksteady battle the turtles before being distracted by casey who leads them into their cell in a chase. april throws sacks back in his cell while the turtles lock in the rest. baxter however gets away with groundchuck and dirtbag.
after preventing prisoners to escape. the turtles start to win the crowd over. the cult ends when they find out the turtles stopped shredder and krang. this allows the turtles to move back into the original lair.the turtles,splinter,april and casey go to tcri for the final confrontation. baxter watches on security and sends groundchuck and dirtbag to fight. karai also makes her way to tcri. shredder comes threw a portal with dead krang revealing that he unthawed himself in the technodrome and killed krang before using a portal to return. shredder throws baxter out of the way and makes him land on top of the other mutagen can.the turtles fight groundchuck and dirtbag and win, knocking them out cold. april and casey sneak threw the lab where they come across karai. she is then knocked out by vernon from behind. cynthia utrom finds the three and battles them before the roof of the lab caves it and traps utrom in rubble while the three head to find the turtles. splinter finds shredder and battles him. meanwhile, the turtles find baxter who has became a fly and a brawl begins. in the end, shredder is decapitated by splinter and baxter is knocked down by the turtles. cynthia presses the emergency button that erases every mutant out of existence. mikey,raph,splinter,groundchuck,dirtbag,bebop,rocksteady and baxter dissapear while leo and donnie head to the top of the building to reverse the button effect. the mutants return and casey arrests baxter,cynthia,karai and groundchuck and dirtbag, who become cell mates to bebop and rocksteady. the turtles are considered heroes and they run off back into the night to face off against bank robbers tokka and rhazar
THE END