Thomas, Twilight, and the Rise of the Planet of the Apes is the second upcoming Thomas/MLP:FIM/Planet of the Apes crossover made by Hiatt Grey. And the sequel to Thomas, Twilight, and the Rise of the Planet of the Apes.
Ten years after the pandemic of the deadly ALZ-113 virus, or Simian Flu, the worldwide human population has been drastically reduced, with only a few genetically immune to the virus. Apes, with genetically enhanced intelligence caused by the same virus, have started to build a civilization of their own. Caesar is the chimpanzee leader of an ape colony in the Muir Woods near San Francisco. Caesar's son Blue Eyes and his friend Ash encounter a man named Carver in the woods, who panics and shoots Ash, wounding him. Carver's party, led by Malcolm, arrive while a number of apes join Blue Eyes and Ash. Caesar orders the humans to leave, and they flee to their community in San Francisco, centered around "the tower", a partially finished skyscraper. Prompted by Koba, a scarred bonobo who holds a grudge against humans for experimental mistreatment, Caesar brings an army of apes to the tower. There, he announces that while the apes do not want war, they will fight to defend their home. He demands that the humans stay in their territory. Malcolm convinces his fellow leader Dreyfus to give him time to take a small team to the forest to reconcile with the apes and gain access to a hydroelectric dam in their territory, which could provide long-term power to the city. Malcolm meets with Caesar, who allows the humans to work on the generator on the condition that they surrender their guns. As Malcolm, his wife Ellie, and son Alexander work, they bond with the apes. Mutual distrust of both sides gradually subsides until Caesar discovers a gun Carver had hidden and orders the humans to leave. He later allows the humans one extra day to work on the dam after Ellie uses medicine to save Caesar's wife, Cornelia.
Distrustful of the apes, Dreyfus arms his community using an armory. Maintaining his distrust of humans, Koba discovers the armory and later confronts Caesar, accusing him of loving humans more than apes. In response, Caesar severely beats Koba, but refrains from killing him. Koba returns to the armory, where he takes an assault rifle and kills two guards. Returning home, he secretly kills Carver. The generator is repaired, restoring power to the city. During the celebration, Koba sets fire to the apes' home then, unseen to anyone else, shoots Caesar, who falls from the settlement's main tree. In the subsequent panic, Koba takes charge, implicating Carver in the shooting and convincing the apes to attack the humans. He leads them into San Francisco, where they plunder the armory and charge the tower. The apes breach the building and imprison the humans as Dreyfus flees underground. When Ash refuses Koba's orders to kill unarmed humans, citing Caesar's teachings, Koba kills Ash and imprisons any ape still loyal to Caesar.
>Malcolm's family finds Caesar barely alive and transport him to his former house in San Francisco. Caesar reveals that Koba shot him, realizing that apes can be as corrupt and violent as humans. When Malcolm sneaks into the settlement to find medical supplies for Caesar, he encounters Blue Eyes, who spares him before learning that his father is still alive. After reconciling with Caesar, Blue Eyes returns to the tower and frees the imprisoned humans and apes. Malcolm leads the apes into the tower, where he finds Dreyfus. He learns that the return of electricity allowed Dreyfus' men to make radio contact with survivors at a military base, who are now coming to fight the apes. Caesar confronts Koba at the top of the tower; as they fight, Dreyfus detonates C-4 charges that destabilize the tower, at the cost of his own life. Koba starts shooting at the apes, but Caesar tackles him off a ledge. While clinging on a metal girder, Koba is rejected as an ape by Caesar and is dropped to his death.
Malcolm and Caesar acknowledge their friendship, with Malcolm warning of the approaching human military. Caesar warns that the humans will never forgive the apes for their attack, and convinces Malcolm to leave with his family. Caesar stands before a kneeling mass of apes.
- Knockout, Puffer, Dolphy, Rachel, Mighty Joe, Daylight, Jenny, Pete, Kevin, Morley, Blitzer, Zecora, Babs Seed, Gabby, Princess Ember, Team Griffin/Eeveelution, Peter Griffin, Dudley Puppy, Kitty Katswell, Judy Hopps, Nick Wilde, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Russell Ferguson, and Buttercream Sunday guest star in this film.
- The storyline concludes in Thomas, Twilight, and the War for the Planet of the Apes.