* Scenes with Will's father that reveal the symptoms of his Alzheimer's disease, especially [[spoiler:after Cure 1.0 fails]].
* The death of [[spoiler: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.
* [[spoiler:Buck's death.]]
* [[spoiler:Due to the DownerEnding described in the Main section, the realization that Caesar will likely soon lose his adoptive father as well.]]
** [[spoiler: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 [[spoiler: attacking Hunsiker to protect Charles. After Hunsiker's daughter comes out, Caesar [[OhCrap 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.