Splinter is saved by Casey Jones and Danny before Tatsu and the Foot Clan can kill him, and after Splinter lectures some of the Foot Clan members about how the Shredder was using them for his own ends and didn't care about them, the three go to help the Turtles. The Turtles, after disposing a great deal of the Foot Clan, face Shredder on the roof of a building, who proceeds to hand their asses to them. When Shredder threatens the life of Leonardo, he tells Raphael, Donatello & Michaelangelo to dispose of their weapons. They toss them over the side of the building, but one of Michaelangelo's nunchakus gets caught on a ladder rung. Just before Shredder can inflict the fatal blow on Leonardo, Splinter appears, and Leonardo rolls away.
Splinter addresses Shredder by his real name of Oroko Saki, and told him how he killed his master Hamato Yoshi. Shredder takes off his faceplate to reveal the scarring Splinter inflicted on him while still a normal rat, confirming his identity. Shredder charges at Splinter, but Splinter whips out the nunchaku and entangles it around Shredder's staff, sending him over the edge of the building but hanging on by his entangled staff. Shredder tries to throw his ankle knife at Splinter, but Splinter catches it, and due to letting go of the nunchaku Shredder falls into a garbage truck, and Casey turns on the crusher, killing him - or so we think
Danny reunites with his father Charles, April O'Neil (Judith Hoag) gets her job at the news company back and kisses Casey, the non-participating members of the Foot Clan whom Splinter lectured tell the police to go to the Foot Clan's warehouse on Laird Island to get their answers, and the Turtles reunite and celebrate with Splinter.
Thanks Tornado Dragon!