The Turtles are in danger of exposure when hot-headed Raphael is caught on video arguing with a human on the street. He must learn to control his temper in order to help the others retrieve the video before it falls into the wrong hands.

The Turtles must defend their home in the sewers when Chris Bradford tries to destroy it with a dangerous chemical.

Snakeweed returns and begins abducting people. Tired of Raphael's constant criticism while trying to stop Snakeweed, Leonardo lets Raphael try his hand at leadership. While away from the group, Leonardo meets a female Foot Ninja named Karai, who tries to lure him to the dark side.

While trying to foil a Kraang invasion plot, the Turtles are hunted by a giant cockroach.

When Shredder plans to create an army of mutants, the Turtles must rely on the help of the Pulverizer, who was recruited into the Foot (to be expendable) and volunteers to gather information on the inside on their behalf. When he agrees to be a test subject for a stolen supply of Kraang Mutagen, the Turtles rescue him, but not before he recklessly gets himself mutated.