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.

As the Turtles search for Karai, they are forced to deal with a city filled with Kraangdroids as well as Zeck and Steranko.

Donnie finishes a new batch of retro-mutagen in hopes of saving Karai; the Turtles are hunted by Shredder's new henchmen, Bebop and Rocksteady.

Karai searches for the legendary Kuro Kabuto, claiming to be the rightful heiress of the Foot Clan, when she suddenly encounters an old rival.

Donnie's grudge with Don Vizioso threatens the Turtle's newest mission.

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The Turtles must train their 80s counterparts into fighting like real ninja. The 80s Turtles begin to learn the difference between their world and the world of their modern counterparts.