Thomas and Twilight Sparkle's Adventures of Terminator 3: Rise of the Machines is the third upcoming Thomas/MLP/Terminator crossover and sequel to Thomas and Twilight Sparkle's Adventures of Terminator 2: Judgment Day to be created by Stuingtion.
John Connor has been living off-the-grid in Los Angeles in the years following the death of his mother, Sarah, from leukemia. Although Judgment Day did not occur as expected on August 29, 1997, John still believes that war between humans and Skynet will occur. Unable to locate John in the past, Skynet sends a new model of Terminator called the T-X back to July 24, 2004 to kill other members of the human resistance. More advanced than previous Terminators, the T-X has an endoskeleton with built-in weaponry, a liquid metal exterior similar to the T-1000, and the ability to control other machines. Unlike previously seen Terminators, its standard appearance is female and Queen Chrysalis and the Biskit Twins arrive to help it out.The resistance sends a reprogrammed T-850 model 101 Terminator back in time to protect the T-X's targets, including Kate Brewster and John. As Stewie's time machine brought Stewie, Dusty Crophopper, the Princesses and the Autobots to help the T-850.
The T-X was able locate Kate and then John at an animal hospital, but they escape with the help of the Terminator and our heroes. The T-X commandeers a crane and several other vehicles and gives chase. After an extended chase and battle in the city, the Terminator and our heroes take John and Kate to a mausoleum where Sarah Connor is interred. Inside her vault they find a weapons cache that was left at Sarah's request in case Judgment Day was not averted. The T-X and police arrive and begin a gun battle, Queen Chrysalis then almost kills Rarity and Pinkie but Mako shoves them out of the way of the blast at the last second and is killed instead. But John, our heroes, and the Terminator escape with Kate in a hearse. Following its programming, the Terminator begins driving John and Kate to Mexico to escape the fallout when Judgment Day begins. John puts a gun to his head and threatens to kill himself after learning that Judgment Day was scheduled to begin at 6:18 p.m. that day. He orders the Terminator to take him and Kate to see Kate's father, an Air Force officer who knows where Skynet is. The Terminator explains that after Cyberdyne Systems was destroyed, Skynet was taken over by the United States Air Force. The Terminator calls John's bluff but agrees to take them after Kate orders him to. Upon questioning, the Terminator reveals that Kate sent him back from the future and that he killed John in 2032.
At the Air Force base, General Brewster faces pressure from the President to activate Skynet to stop a malicious computer virus that is infecting computers all over the world. John, our heroes, and Kate arrive too late to stop Skynet from being activated, then Princess Celestia uses the Blue Ruby and Black Pearl to resurrect Mako in the nick of time, and the Air Force machinery begins to massacre the staff members. But our heroes manage to destroy most of them. Colonel Brewster is mortally wounded by the T-X, as it arrived before John, Kate, our heroes, and the Terminator. Before dying he gives Kate and John a code book and the location of what John believes is Skynet's system core. John and Kate head for the tarmac to take an airplane to reach Crystal Peak, a military base built into a mountain that's hardened against nuclear attack. The T-X and Terminator clash in battle, and the T-X beats him badly before taking over his system. The T-X pursues John and Kate through the military base but becomes trapped when a particle accelerator at the facility is activated and the magnetic field bonds it to the accelerator. In the hangar, the Terminator attacks John and Kate before John and our heroes convince it to reject the T-X's control which shuts it down.
John and Kate reach Crystal Peak and begin entering the access codes to gain entry when the T-X arrives by helicopter. Just as she's about to attack them, the rebooted Terminator arrives a few minutes later in a second helicopter which crashes into the T-X, ripping it in half. The T-X pulls itself from the wreckage and attempts to drag itself inside the bunker and follow John and Kate. The Terminator holds the bunker open long enough for John, our heroes, and Kate to lock themselves inside, then he uses his nuclear power cell to destroy both himself and the T-X as well. Once inside Crystal Peak, John, and our heroes, and Kate discover that the facility isn't Skynet's core, but instead is a nuclear fallout shelter and that Skynet has no core. Judgment Day begins outside, as nuclear missiles are fired at several locations around the world, killing millions and they begin receiving radio transmissions on the emergency equipment inside. John assumes leadership and begins answering radio calls, as he muses in a voiceover about how he realizes now that the war with the machines could never be avoided.
- Stephen, Zecora, Button Mash, Daring Do, Steamy, Puffy, Evan, Shai-Shay, Rattlesnake Jake, Mako, Willy, Sharky, T.C., Hugs, Sherin, Jenny Wakeman, Dudley Puppy, Kitty Katswell, General Dedrich, Marshall P.F., The Miner Trains, The Planet Trains, J.J., Buzz, Lazlo, Raj, Clam, Ed, Edd n', Eddy, Anna, Elsa, Wreck-it Ralph, Vanellope von Schweetz, Fix-it Felix, Sargeant Calhoun, The Powerpuff Girls (Blossom, Bubbles, and Buttercup), Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, Russell Ferguson, SpongeBob SquarePants, Patrick Star Dusty Crophopper, Princess Celestia, Princess Luna, Optimus Prime, Bumblebee, Ironhide, Ratchet, Dino, Sideswipe, Skids & Mudflap, The Wreakers, Arcee, Wheelie, and Brains guest star in this film.
- Queen Chrysalis will work for the T-X in this film.
- The storyline continues in Thomas and Twilight Sparkle's Adventures of Terminator: Salvation.
- This takes place after Brian and the Eeveelution Family's Adventures of the first three Transformer films, because the LPS gang already knew the Autobots.