When Donatello's latest invention gives failed inventor and perpetual loser Baxter Stockman enhanced abilities, the turtles must learn to use their heads instead of brute force to defeat him.

When Donatello loses confidence in his bo staff as an effective weapon, he constructs Metalhead, a fully armed robotic turtle based on Kraang technology.

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

When simultaneous threats from the Purple Dragons and Baxter Stockman’s mechanical Mousers force the Turtles to split into two groups, Donnie & Mikey must prove that their “B Team” is just as valuable as Leo & Raph’s “A Team.

Michelangelo befriends Leatherhead, an unstable mutant alligator who possesses a strange piece of Kraang technology, but the other Turtles aren’t sure whether Leatherhead is a friend or a foe.

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.

The Turtles believe they have defeated most of their old enemies, but they soon discover that a new evil is rising from the ashes.

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