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Tear Jerker: Rise of the Planet of the Apes
Scenes with Will's father that reveal the symptoms of his Alzheimer's disease, especially after Cure 1.0 fails.
The death of Will's father, who refuses to take Cure 2.0, signalling to his son that it was perhaps time to let go.
Arguably made worse by the fact that the scene is completely wordless.
Caesar being separated from Will for the first time at the primate shelter.
Caesar learning that his mother died.
Due to the Downer Ending described in the Main section, the realization that Caesar will likely soon lose his adoptive father as well.
Franklin's death. He was one of the only people at the facility who actually cared about all the apes, yet he dies a slow and probably agonizing death as the first victim of the plague.
The immediate aftermath of Caesar attacking the neighbor to protect Charles (Will's father). After the neighbor's daughter comes out, Caesar realizes that he made a mistake, and goes over to hug Charles. The expressiveness on his face is just gut-wrenching in this scene.
Everything about the attic window that Caesar draws on the wall of his cell.