- The fact that there are apes who betrayed Caesar and chose the Colonel's side.
- The Colonel murders Cornelia and Blue Eyes, originally intending to kill Caesar.
- Caesar's entire struggle with his dark, vengeful desires. It's sad to see such a noble character being continuously tempted into Jumping Off the Slippery Slope, and being fully aware of it as it's happening.
- The death of Luca. He dies knowing he protected Caesar this time.
- Bad Ape recounting when the Colonel and his troops have been killing other Evolved Apes. He sounds almost shell-shocked."Human get sick. Ape get smart. Then human kill ape. BUT NOT ME! I run!"
Caesar: You learn to speak?Bad Ape: Listened. Human: (impersonating human captor) BAD APE! (points to himself) Bad ape...
- The humans' brutality is further established when he speaks of the "human zoo".
- The Colonel himself, depending on whether you sympathize with his motive and what started his descend to darkness. He's been desperately trying to stave off the Simian Flu by hunting down evolved apes and killing humans infected by the mutated virus that would devolve them into voiceless animals and rob their humanities. Eventually, his effort is proven to be futile as the Colonel himself ends up infected by the very virus he's been trying to fight against, and he locks himself in his quarters as he's reduced to a defenseless, ill, unintelligent, pathetic shirtless drunk. When Caesar confronts the Colonel and is about to shoot him, the Colonel stands by his convictions, pulling back the hammer and urging Caesar to kill him, only for Caesar to refuse. Plagued by his loss of the only thing that makes a human a human: the ability to speak, the Colonel tearfully shoots himself in the head. It's hard not to feel sorry for what happened to him towards the end. In the end, he's just a human trying to safeguard his sense of humanity, only to be denied.
- Right before Caesar even finds the Colonel, he sees a mess made in his quarters including many dropped bottles of whisky and even a picture of the Colonel's son as a child on the table. He finds the Colonel in the next room over, passed out on his bed after having drank too much...and then comes The Reveal that the Colonel can't speak and that he had contracted the virus. The implication is that the Colonel noticed when the symptoms were starting in him and knew full well that he was infected by the same virus that had claimed his son, and it had driven him into an emotional breakdown. Psyching himself up to killing himself, he'd drowned out his fear and sorrow about what he was going to become in alcohol - the last drinks he'd have as a regular human, in his last moments as a regular human. We're never shown the man's breakdown on screen, but are shown all we need to know about what it must have been like for him.
- Caesar dying at the end. It's at least made somewhat better with him knowing that the apes and his son are now in a safer home.
Maurice: Son...will know...who... was...father. And what...Caesar...did...for us.
- Doubly so as Maurice, who at this point has spoken very little, extendedly voices to Caesar that his son will know just the kind of ape and hero he is.
- A deleted scene included in the Blu-ray of the film revealed Malcolm's fate. Malcolm met with the Colonel in an attempt to stop war from escalating and that peace should be made with Caesar, only to be killed in cold blood.
Tear Jerker / War for the Planet of the Apes