The Turtles are heading through the sewers when a laser blasts Leonardo off his feet, followed by Raphael being shot in the back. Michelangelo disarms two of them, only to be shot in the backside by a third.
In the lair, Donatello and Professor Honeycutt are going over the new security system, and the Fugitoid thinks that they need to toughen up the surveillance lasers since Michelangelo was able to disable them so easily.
They reflect on Leatherhead's attack on Honeycutt on Burnow Island, and the other problems they have with the Mutanimals and Alopex (leading to Michelangelo teasing Raphael again about Alopex). They also discuss the immortal siblings who have caused chaos in their lives, as well as the enemies - mutants, human and government agencies - who are still out there.
Unbeknownst to the Turtles, a figure is slithering through the sewers, where it disables one of the lasers with glowing tentacles. The lights go out, and when Donatello turns on a flashlight, a tentacled alien creature is hanging from the ceiling, holding Honeycutt prisoner. Donatello tries to restore the lights while the other Turtles attack the alien, but with little effect.
Honeycutt reveals that the alien is a bounty hunter from Dimension X named Hakk-R. The bounty hunter interfaces with Honeycutt's electronic body and downloads the identities of the various witnesses being called for Krang's trial, just before Donatello sets him on fire with an aerosol can and a welding torch. It teleports away.
Honeycutt says that he must tell the king of the Neutrinos about what has happened, and that they must save the witnesses lest Krang go free. Leonardo declares that they're not about to let Krang get away with his war crimes, and that they're going to help him by going to Dimension X once more.