*In the present, the Teenage Mutant Ninja Turtles grow apart after defeating the Shredder. For training, Master Splinter sends Leonardo to Central America, where he becomes the protector of a village, to which the villagers refer to him as the "Ghost of the Jungle". Donatello works as an IT specialist, Michelangelo works as a birthday party entertainer named "Cowabunga Carl", and Raphael continues to fight crime as a masked vigilante known as the "Nightwatcher", which he keeps a secret. The Turtles' old friend April O'Neil now operates a shipping company that acquires relics for collectors, assisted by her boyfriend, Casey Jones.

After traveling to Central America for work, April tells Leo his brothers have drifted apart. She then returns to New York City with a statue for wealthy tycoon Max Winters. Winters hires Shredder's former second-in-command, Karai and her ninja Foot Clan to search the city for the thirteen monsters before the portal opens again. Casey figures out Raph's double identity and joins him in hunting criminals. Winters, who is actually Yaotl, reanimates his four stone generals using technology created by his company.

Leo returns to the Turtles' sewer lair, reuniting with his family. Splinter forbids them from fighting crime until they can act as a team again. While training, the Turtles encounter one of the thirteen beasts, Bigfoot. They engage Bigfoot, disobeying Splinter's orders, and come into conflict with the Foot Clan in the process. While the Turtles and ninja fight, a fleeing Bigfoot is captured by the generals. The next day, Splinter admonishes his sons for their disobedience.*