The Teenage Mutant Ninja Turtles begin their journey as a true team of brothers, although distance still remains between them. Meanwhile, Baxter Stockman and General Krang have largely kept in the shadows... until now. General Krang wants results and Baxter has a new invention to capture the Turtles before Krang comes to New York.

Krang, Baxter Stockman, Old Hob, and Alopex all get their turn. Krang's history is revealed, Baxter's secret project may be more dangerous than he realized, Old Hob is ready to branch out on his own, and Alopex discovers a devastating truth about her past.