A successful raid on an Earth Protection Force train ends up being the final straw for the President of the United States, who threatens to cut the organization's funding for their repeated recent failures.
Unknown to Bishop, however, the residue from the destroyed alien clones leaks into New York City's sewers, and after coming into contact with local fauna, mutates them, triggering a massive mutant outbreak.
During this outbreak, Baxter Stockman finally clones a new human body for himself, but it along with his sanity deteriorates, and he eventually drowns in the Hudson River while attacking April O'Neil.
In the meantime, Leo's emotional scars drive him to become progressively more hostile and surly to the point of wounding Splinter in an uncontrollable rage during a training session.
The Ancient One, having foreseen the attack, sends Leo back to New York, where he reunites his family and finds them a new home before defeating Karai, vowing that any further conflict between their clans will result in her death.
Bishop agrees, but charges the Turtles with retrieving the Heart of Tengu, a relic possessed by Karai that an unknown entity has promised will grant him centuries of advancement in technology.