Some TMNT stuff really isn't for little kids.
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Raphael and Zak continue leading the frontal assault, while Leonardo, Michelangelo and the Neutrinos have reached the room where the King and Queen are being held, guarded by General Krang. Leonardo manages to slice off one of Krang's robotic suit's arms. Krang recognizes the Turtles as the ones that were stolen from Stockgen.
Back in the lab, Donatello and Honeycutt have almost finished repairing the END missle. Donatello is telling Honeycutt how he's skeptical that he and his brothers are reincarnations of four boys from Feudal Japan. Honeycutt explains to him how teleportation works; how each individual atom is scanned, destroyed, and an exact copy built in the new location. Despite being intangible, the soul is always intact and present after the teleportation process, something even their advanced science cannot explain. Honeycutt supposes that if the soul can make the journey across dimensions, it's possible it couldn travel across space and time as well.
Back on Burnow Island, Karai's infiltration and theft of some of the Utrom ooze is discovered while she makes her escape back to Foot headquarters.
Raphael and Zak are continuing to lead the frontal assault when they're set upon by a huge Utrom mecha. The NRF forces in the attack are under heavy fire and the situation looks grim. Honeycutt and Donatello have finished the END missle and launch it towards the battlefield, following it to ensure it isn't struck down. The Utrom mecha is about to swat it down when Raphael takes it out with a rocket launcher, allowing the END missle to detonate and disable all of Krang's troops' weapons. In the Neutrino royal castle there is a standoff between Krang, his forces, the Turtles and the NRF. Honeycutt arrives and says he has neutralized Krang's entire army, effectively winning the battle. However, Krang reveals that his weapons operate on a different frequency, meaning he still has lethal firepower. Honeycutt gives himself up to spare the others, and Krang teleports back to Burnow Island with him. The Neutrinos thank the Turtles for their help, and Michelangelo gets a kiss on the cheek from Princess Trib.
Back at the Turtle's home in New York City, April and Casey are worrying that the Turtles are gone for good, when suddenly they teleport back from Dimension X. Everyone is glad to be reunited.