"Battle for New York, Part 1" is the twelfth episode of the third season of the 2012 TV series, the sixty-fourth episode overall in the series, and is also is part 1 of 2 of the mid-season finale of Season 3. It first aired on March 15th, 2015.
The episode begins as Mikey is in Donnie's lab trying to make Plutonium for retro mutagen by stuffing different things in it. When Donnie sees what Mikey's doing to the retro mutagen he is enraged. He tries to stop his brother, but one drop of it falls in the retro mutagen, which starts to bubble and foam; it looks like it will explode, but instead it sparkles. Donnie angrily tackles Mikey and the two tussle until Splinter comes and pressure points both of them, demanding to know what is going on. Donnie scans the mutant cells and reveals that Mikey's Plutonium perfected the Retromutagen. Also it takes a drop of Retromutagen to a whole canister of regular mutagen. Donnie asks what did he use but Mikey only remembers using pizza, urinade, analite, and muronic acid. When Donnie is about to berate him, Master Splinter says that Mikey's tomfoolery made something that can save New York City, but April points out that they are in Dimension X due to the dreams she had.
The Turtles plan to go to the TCRI, use their dimensional portal to enter Dimension X, and save the people. Donnie tells them the invention that could save New York, but it turned out to be a water tower. But when Donnie tries to explain his invention, a Kraang Stealth Ship appears causing the Turtles to hide. The Kraangs are still searching for humans. Two humans were spotted and were captured by the Kraang. The Kraang is about to mutate them until Leo saves them. The couple screams and runs away despite him saving their lives. The other Turtles come out and try to fight them but they are outnumbered, but a breadcrumb was thrown and when the Kraang inspects it, Pigeon Pete comes out. Soon Leatherhead, Dr. Rockwell, and even Slash come and save them, calling themselves The Mighty Mutanimals. Leo scolds him for using Pete as bait and they get into a fight. Slash claims that he was different as the mutagen messed his brain up. Leatherhead and Mikey backed them up saying everyone deserves a second chance. They follow the Mutanimals back to their lair.
At the Mutanimals lair, Jack Kurtzman appears and is revealed to have survived the invasion. He wants the Ninja Turtles and Mighty Mutanimals to team up, much to both leaders' objections. Kurtzman stops their fight and explain's that the Kraang are building a mutagen missile that could transform Earth into another Dimension X. But everyone begins to fight until the Kraang shows up, this time with Biodroids. During the fight Kurtzman tries to get the Kraang intel disk only for him to get shocked by a stray blast much to everyone (especially Pete's) despair. Leatherhead comes to his aid, while both teams leave.
At the Turtles hideout, Kurtzman, who is still alive, gives Leo the Intel disk before he falls unconscious. Splinter, April, and Casey will stay and help Kurtzman while both teams figure out how to stop the missile. Donnie comes up with the idea of hacking it into the missile and disabling it. Slash wants to attack the Kraang first while, Leo suggests taking out the missile sky high. Slash decides to do it his own way. Donnie takes the Turtles to the water tower only to reveal that it is Donnie's new invention, the Turtle Blimp.
Meanwhile, at the missile site, Kraang Subprime asks why it took so long, and the Kraang state that most of the perfected mutagen supply was used in the Invasion. Suddenly the Mutanimals arrive and attack the Kraang. Raph comments that the Mutanimals attack is the perfect distraction for them. Despite their best efforts Kraang Subprime was able to launch the missile. Donnie managed to reset its coordinates to the heart of the sun, and they fall and use their gliders to get to safety. While Pete was celebrating their victory, the Irma-head comes to life and tries to shoot Pete until Slash destroys it. Kraang Subprime orders his troops to retreat and they escape. Both teams celebrate their victory. Leo is watching Slash the whole time, and was impressed by Slash's bravery and sticking up for his teammates. Now they have to break in TCRI, and save New York City, and quite possibly the world.
"Donatello: Mikey, HAVE YOU LOST YOUR SHELL?!"
"Raphael: Is that all you got? (Kraang shoot lasers) Apparently not!"
"Kraang Subprime: You guys are as dumb as a box of rocks! Seriously, what's taking you so long?! It's been three months! Kraang: Much of Kraang's mutagen supply was spent in the invasion of the city known as New York City. Kraang Subprime: What is it with the "Kraang's invasion of the city known as New York City"? What is that? We've been here for thousands of years, YOU CAN'T EVEN SPEAK PROPER ENGLISH!? Kraang: Kraang does not understand the query known as Kraang Subprime's query."