Thomas, Twilight, and the War for the Planet of the Apes is the third and final upcoming Thomas/MLP:FIM/Planet of the Apes crossover made by Hiatt Grey. And a sequel to Thomas, Twilight, and the Dawn of the Planet of the Apes.
Some time after the U.S. military was called to fight off an increasingly intelligent and dangerous army of apes, the apes' clan, led by the chimpanzee Caesar, is attacked in the woods by a military faction known as Alpha-Omega. Apes who followed Koba, who previously led a failed coup against Caesar, have joined Alpha-Omega. Some of the militants, including the gorilla Red, are captured, but Caesar releases them as a peace offering to the humans. Learning that Alpha-Omega follows the leadership of a ruthless Colonel, Caesar plans to relocate the clan across the desert, not wanting to suffer any more ape casualties. The night before their journey, Alpha-Omega infiltrates the apes' base and the Colonel kills Caesar's wife Cornelia and their elder son, Blue Eyes.
Leaving his younger son, Cornelius, in the care of Blue Eyes' mate, Lake, Caesar departs to exact revenge on the Colonel. He is accompanied by Maurice the orangutan, Luca the gorilla and Rocket the chimpanzee, while the other apes head for the desert. Caesar's party confronts traitorous albino gorilla Winter in an Alpha-Omega camp and learn that the Colonel has departed for a location called the "border." Caesar inadvertently asphyxiates Winter, which causes him to worry that he is becoming like Koba.
During their journey, they encounter a man living alone in an abandoned village and kill him when he reaches for his rifle. They then discover his young daughter, who is apparently unable to speak. Maurice insists that they take her with them. Further along, they discover some Alpha-Omega soldiers that have been shot and abandoned. Their examination of a survivor reveals that he, like the girl, cannot speak. In an abandoned souvenir shop, the group meets Bad Ape, a chimpanzee hermit who lived in the Sierra Zoo before the Simian Flu pandemic. Bad Ape is able to direct them to the border, a former weapons depot that was turned into a quarantine facility when the virus first began to spread.
When the group arrives at the border facility, Luca is killed protecting Caesar from an Alpha-Omega patrol, motivating Caesar to proceed alone. However, he is captured by Red shortly after witnessing the rest of his ape clan being forced to build a wall with no food or water. The Colonel reveals to Caesar that the Simian Flu virus has mutated and now causes humans who survived the original strain to become mute and regress back to a primitive state, and that he is barricading himself in the facility to fend off rival military forces coming to defeat him because he favors killing any infected humans – including his own son – to stop the spread of the virus.
While Caesar is tortured with starvation, the mute girl, whom Maurice names Nova, sneaks into the facility to give him food and water. To prevent her from being discovered, Rocket allows himself to be captured as a diversion. Together, Caesar and Rocket are able to work out a means of escape via an underground tunnel that leads out of the facility. Maurice and Bad Ape use the tunnel to rescue the . Caesar orders the others to escape while he goes to confront the Colonel, but the facility comes under attack by the rival military forces. When Caesar reaches the Colonel, he realizes that the Colonel has been infected by the mutated virus. Caesar ultimately spares the Colonel, who takes his own life rather than exist as an infected primitive.
During the battle between Alpha-Omega and the rival militants, the apes attempt to escape, but are noticed by Alpha-Omega soldiers, who turn their fire upon the apes. Caesar attempts to attack Alpha-Omega from behind, but is shot by one of the militants he had previously set free. Red saves Caesar's life at the cost of his own, and Caesar blows up the facility's fuel supplies, causing a cascading explosion which wipes out Alpha-Omega and allows the rival militants to triumph. The rival militants almost shoot Caesar, but are distracted by an avalanche, which buries the human forces. Caesar and the other apes (carrying Nova) survive by climbing nearby trees.
The remaining apes depart the facility and cross the desert to find a paradise-like oasis. While the other apes joyously celebrate their new home, Maurice discovers Caesar's wound, and assures Caesar that he will be remembered as Caesar quietly passes away.
- Knockout, Puffer, Dolphy, Rachel, Mighty Joe, Daylight, Jenny, Pete, Kevin, Morley, Blitzer, Dile, Zecora, Babs Seed, Gabby, Princess Ember, Duck, Oliver, Toad, Donald & Douglas, Stepney, Daisy, Ryan, Arthur, Murdoch, Rosie, Mavis, Jack, Alfie, Skarloey, Rheneas, Sir Handel, Peter Sam, Rusty, Duncan, Duke, Smudger, Bertram, Mighty Mac, Fearless Freddie, Team Griffin/Eeveelution, The Griffin Family, Vinny Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Little Bear, Duck, Cat, Owl, Hen, Emily (Little Bear), Lucy, Doug Funnie, Skeeter Valentine, Natsu Dragneel, Lucy Heartfilia, Erza Scarlet, Gray Fullbuster, Wendy Marvell, Happy, Carla, Bob the Builder, Scoop, Muck, Dizzy, Roley, Lofty, Spud the Scarecrow, Travis, Ed, Edd, n Eddy, Dudley Puppy, Kitty Katswell, Hanah Streaker, Roberta Bravo, Judy Hopps, Nick Wilde, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Russell Ferguson, Buttercream Sunday, Gail Trent, Mitzi, Sugar Sprinkles, Captain Cuddles, Jasper Jones, Sue Patterson, Youngmee Song, Belle, Ariel, Jasmine, Princess Anna, Queen Elsa, Tempest Shadow, Grubber, Songbird Serenade, Capper, Captain Celaeno, Princess Skystar, Queen Novo, SpongeBob SquarePants, Patrick Star, Squidward Tentacles, Sandy Cheeks, Mr. Krabs, Blackie, and The Powerpuff Girls guest star in this film.
- Queen Chrysalis, the Changelings, Ernie the Giant Chicken, Alter, Samantha & Slate will work for the Colonel in this film.
- Thomas, Twilight, Brian, Cadance, Shining Armor, Puffer, and Jenny will be taken with Ceaser in this film.