The aftermath of the first battle in the beginning of the film. The apes' sanctuary is a smoldering ruin, ape corpses litter the battlefield, and the surviving apes are wounded and frightened, reaching out to Caesar for reassurance as he arrives. War Is Hell, indeed.
The fact that there are apes who betrayed Caesar and chose the Colonel's side. The tragic irony is that most of these were Koba's followers, and fled to the Colonel out of fear of Caesar. They're now forced to fight for humans against their own kind, which is the last thing that even Koba would have wanted. Unless Caesar's hallucination of him saying the apes are doomed is accurate.
Blue Eyes and Cornelia's death. Especially Blue Eyes, an important character in the previous film who had plenty of character development and looked every bit a worthy successor to his father's legacy. He is unceremoniously gunned down by Alpha Omega when they raid the ape base.
Caesar finally finding baby Cornelius alive and well after witnessing the deaths of his wife and eldest son. The mighty ape leader is reduced to inelegant sobs as he hugs his child, the only family he has left, telling him how much he loves him and how he's safe now.
Winter's betrayal. He may have been a Dirty Coward who ratted out his fellow apes to save his own behind, but it's still quite sad to see him pleading to Caesar for forgiveness, and later being accidentally killed by Caesar who ends up suffocating him to death while trying to silence him when hiding from the human soldiers.
Winter's death weighs heavily on Caesar, who is later tormented by nightmares of Koba, mocking him with the line, "Ape not kill ape".
Koba may be dead, but his presence and dark legacy is very much still felt. The entire war was instigated by him in the first place. And Caesar feels himself becoming more and more like Koba as he is fueled by his hatred of what cruelty the humans are capable of.
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. What makes it worse are his nightmares of Koba: the ape who started the war, the ape whose hatred had consumed him like it begins to do with Caesar, the ape whose actions continue to be felt long after his death.
Caesar shoots Nova's father in self defense when he turns a gun on them. The guilt is apparent on their faces when they realize he had a child who would not survive on her own.
The death of Luca. He dies knowing he protected Caesar this time.
Earlier, he bonds with Nova in a heartwarming moment when he picks some flowers and sticks them hin her hair in an affectionate gesture. When Luca is killed, Nova is visibly distraught, putting the flower Luca gave her on the deceased gorilla's head. They didn't have much time together but it was clear in the short span of time she came to see them as family.
In the aftermath of Luca's death Caesar is visibly enraged. Rocket and Maurice become a Good Cop/Bad Cop to Caesar, with Rocket insisting they continue so Luca's death will not be in vain, while Maurice tries to discourage Caesar on his pursuit of revenge as his hatred is costing other apes their lives. What ultimately riles up Caesar to rush off on his own? Maurice telling him "You are starting to sound like Koba."
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!"
The humans' brutality is further established when he speaks of the "human zoo".
Caesar:You learn to speak?
Bad Ape:Listened. Human: (impersonating human captor) BAD APE! (points to himself) Bad ape...
Bad Ape's condition. He's nearly hairless, he's skinny, he's clearly not psychologically sound, anfd he's been isolated so long he doesn't even understand sign language that the apes use to communicate and thus can only speak with Caesar, who knows English. He also joins the group in search for a child he says is in the "human zoo". Said child is never found.
Caesar finding one of his ape scouts crucified and on the verge of death. Said scout barely manages to warn him of the danger before he succumbs to the cold and starvation.
The apes in the prison can't even bear to look at Caesar when he's thrown into the pen with them. The Broken Pedestal status is very evident as Caesar realizes that by leaving the colony on his quest for revenge, he had abandoned his people and left them vulnerable to being captured. Cornelius crying out for his dad in the cage where the baby apes are kept cements the My God, What Have I Done? in Caesar, who realizes too late how selfish he had been.
Caesar standing up for an elderly orangutan being whipped at the prison. He yells "Leave him!" in his usual fearsome voice, and for a moment there is a Hope Spot as the other apes, encouraged by his defiance, momentarily look like they are about to be rised into rebellion...and then the Colonel coldly shoots the elderly orangutan dead in front of everyone and points a gun at Caesar's head. Lake has to plead with the other apes to continue working to spare Caesar's life.
The Colonel himself, depending on whether you sympathize with his motives and what started his descent 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 them of their humanity. Eventually, his effort is proven to be All for Nothing 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 ability to speak, the Colonel tearfully shoots himself in the head. It's hard not to feel sorry for what happens 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 the mess he 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 with copious amounts of 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.
Caesar was mortally wounded and bleeding from the arrow Preacher shot into him, during the entire duration of the ape exodus across the desert. Yet he takes priority in making sure his people make it, he puts their well-being above his own, and it ultimately costs him his life.
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.
Maurice:Son...will know...who... was...father. And what...Caesar...did...for us.
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 the war from escalating and that peace should be made with Caesar, only to be killed in cold blood.
Alpha Omega, during their battle with the Northern Army, spot the apes escaping and begin firing at them. Several apes, including babies, are killed in the ensuing scuffle.
Preacher, the very human Caesar spares early on in the film, later tries to kill him in cold blood. Caesar spared him to show the humans that "we apes are not savages", only for him to show Caesar what an Ungrateful Bastard he is and how humans are even worse savages than the apes can ever be. No Good Deed Goes Unpunished, ladies and gentlemen.
Red Donkey's Heel–Face Turn and resulting Redemption Equals Death. He blows up Preacher, who is preparing to finish Caesar off, and stares defiantly at Caesar as he is promptly executed by the human soldiers for his betrayal.
The total destruction of the Northern Army. While they hate Apes just as much as Alpha Omega, they are at least still decent human beings who risk their life to protect infected humans like Nova. It's saddening to see their moment of glory being cut short by an avalanche that comes out of nowhere.
There's also the fact that in a post-apocalyptic setting, where mankind is a dying race, the main war in the climax is not humans fighting apes, but humans fighting humans. Even on the brink of total extinction, humans still use their remaining resources killing each other over petty ideals. And ultimately, neither side wins.
