It's the Turtles' fifteenth birthday and they're itching to venture up to the surface and showcase their ninja skills. Master Splinter reluctantly agrees. At first, they love the surface with its weird lights and even stranger food (like pizza). However, things go awry when they witness a girl and her father being abducted by men in a van. They try to intervene, but don't fare well during the fight, with the van getting away, only to discover that the kidnappers are really robots with living brain creatures in their chest and were carrying the ooze that made them into mutants.

Eager to learn more about this strange connection, they regroup and begin to practice fighting as a team with Master Splinter appointing Leonardo as The Leader. After storming the enemy fortress, they learn that these creatures are called "The Kraang" and have sinister plans in store. They manage to rescue the girl, April, but The Kraang still have her father. They vow not to rest until they rescue him.

However, the Turtles' attack has not gone unnoticed by the media, which alerts The Shredder to come to New York City to take on Splinter/Hamato Yoshi's students himself. What ensues is the escalating war between the Foot and Hamato Clan, a Myth Arc that turns out to have been in the works for far longer than most of the cast knows, as well as the unraveling mystery of the Kraang's agenda for Earth and humankind. Booyakasha!