When Blue Eyes and Rocket return from their scouting trip, Winter is adamant that the apes leave their hideout for the desert that night instead of waiting, and seemingly out of impatience, he leaves and sells out the apes' location to the soldiers, allowing the Colonel to attack. Why would Winter resort to betraying the apes now when he knows they have a way out? Simple, he didn't. Winter had already betrayed the apes and given up their location by this point, likely the moment he let Red escape, as he didn't know at the time that the apes would find an escape route. Now that they have one, Winter wants them to leave immediately because he regrets his decision and knows the Colonel is going to attack, but it's simply too late to reverse it now.
After teasing a Heel–Face Turn throughout the movie, Preacher remains true to his nature by the movie's end and fatally wounds Caesar. While it may shock viewers at first that Preacher ended up just being a Red Herring, McCullough makes it known to Caesar early on that the soldiers who questioned his morality had already either deserted him or got killed. Since Preacher falls into neither camp, it becomes apparent that, as ambivalent as he looks and acts, he's ultimately just as indoctrinated as every other remaining soldier, so a Heel–Face Turn was never even a possibility.
Bad Ape's assumption that Nova reminds Caesar of himself is actually very accurate. Caesar was adopted by Will after the latter's experiments caused the former's mother to go berserk when she was still pregnant with him, which directly leads to her (being gunned to) death. Caesar (technically Maurice) adopts Nova after Caesar guns Nova's father in self-defense. Interestingly, the genders of the parent and child are gender-swapped.
Despite the title of the movie being War for the Planet of the Apes, there is no all-out final battle between mankind and apes for control of the planet. Instead the major war takes place between two factions of humans with different ideas on how to save their species, with the apes caught in the middle. The title makes sense in Exact Words because whether the apes wage war or not, the planet already belongs to them. Humanity just hasn't figured that out yet, and thinks it can still go back to the way things were.
If this was truly the end of the human race, then one of the last recorded human songs played in an audio machine (if not the very last) was "Hey Joe" by Jimi Hendrix. Probably not a deliberate action of the general, but clearly a good choice.
Why did the Colonel take the infected doll into his room? Because cage where he found her (the one where he kept Caesar) is the place where he killed his son. If you look closely, you can see an old blood stain there. The Colonel thought that this doll belonged to his son. As he said before, all things of infected people were burned. He wanted to remember his child by it.
If you think about it, the ideology of Alpha-Omega is all about the Colonel honoring his son. His son is symbol of Jesus Christ to him and to his army. Look closely:
His soldiers have a tattoo/symbol of Alpha-Omega on same place where he shot his son, the apes who join him have to take the same tattoo and one on their backs which says "Donkey." Why donkey? Because, in the Bible, Jesus rode a donkey. The Colonel wears necklace with a cross over his military dog tags. Every morning, he stood in front of his soldiers without his shirt, not because he was playing on God. He reminded them of the sacrifice of his son (just as Jesus sacrificed himself on the Cross). And out of some sort of revenge, he crucified apes, too.
Why doesn't the Colonel kill himself before Caesar arrives? He's shown to be a rather devout Christian. Killing oneself is considered a sin in some Christian denominations and will bar one from going to Heaven. The Colonel is likely waiting for someone to break in and do the deed for him because he doesn't want to end up in the other place. Even if it wasn't Caesar, his men would have likely done the same due to them following his ideals.
Once Caesar arrives into the Colonel's room, there is the photo of his son John as a small child on table. Whole soaked in the alcohol. Then Caesar finds the Colonel in the next room over, completely drunk, trying to reach the bottle. This could be a hint that the Colonel had been Drowning My Sorrows ever since his son's death. At the time, even if he believed killing him was necessary, he still mourned for his loss. And in his own last moments, his grief and guilt completely crushed him.
The avalanche seems like an Ass Pull. But when you think about it it’s a fitting end for the very last time we see humans, other than Nova, in the trilogy. From the get-go everything just gets progressively worse. It all starts by simply trying to find a cure for Alzheimer’s which leads to a virus that wipes out most of humanity. The few survivors are able to rebuild something close to a civilization, but their power source is running out. They’re able to make diplomatic relations with the apes, only for an Ax-Crazy one to start a war that kills many of them and destroys any hope they had of rebuilding a meaningful society. Then the survivors of that can’t even figure out how to work together against a common enemy. Meaning that an out of nowhere avalanche killing what little is left seems like a fitting end.
A possible explanation for the human army from the north appearing entirely to be The Faceless and The Speechless, and attacking in an obsolete and wasteful Zerg Rush tactic, would be that the attacking force consisted entirely of soldiers afflicted with the mutated Simian Flu and all have lost their ability to speak, but the north leadership have discerned that the virus only destroys speech and not intelligence, so all the soldiers were heavily masked to prevent the virus spreading to any remaining uninfected humans, and these infected soldiers then were all dispatched to be sacrificed as Cannon Fodder against Colonel McCullough's rogue force. So the remnants of the human army were getting rid of two birds with one stone.
Though they cheer loudly (Nova, the shot infected solider, and then McCullough himself were only able to make raspy, gasping sounds), and you can clearly hear several "YEAH!"s as they holler. Which leads to its own Fridge Horror: Maybe the Northern commanders were right, and the new plague can be dealt with medically. Not only did McCullough potentially kill his troops for no reason, there is a cure... or was, since with the Northern army now wiped out, it likely died with them.
Related to an above Fridge Brilliance regarding the eponymous "War." Humanity's last act as a species isn't anything constructive. . . it's another war against themselves. A pointless, stupid pissing contest over who's "right." Humans go out fighting each other to the death.
The most horrifying part? It completely justifies Taylor's iconic breakdown in the original film, that humanity ultimately blew itself up. What we saw in "War" was a mere taste of this complete breakdown of human society.
How McCullough deals with the virus. It's not just the killing of those that are infected, it's that he came to the conclusion that humanity is doomed to be permanently mute. Who knows, maybe over time mankind will become resistant to the virus and regain the ability to speak. Maybe mankind will build up an immunity to the virus, or maybe there are individuals that are immune to the new strain of the virus. Instead, McCullough just removes all those infected. Basically little or no hope for a resistance to the virus to be built up.
There's no actual evidence that the virus destroys higher reasoning abilities, instead of just making people mute. In fact, the signs indicate the contrary, as Nova is capable of a whole range of emotions and can learn sign language, and even the Colonel admits that he saw love in his son's eyes after he became mute. The Colonel murdered people for no reason.
However, the prequel comic features a surgeon that went feral after being infected with the mutated form of the virus, and another scientist, Dr. Peter Burke, comes to conclusion that the second wave of Simian Flu indeed affects people on the cognitive level. This is a new form of Fridge Horror: what if the Colonel is right?
It also brings up another Fridge Horror in what that would mean for poor Nova.
Even if Caesar and his group hadn't come across Nova's father or had spared him, he still would have gotten infected due to being in close contact with her.
As heartwarming as all their scenes together are, Maurice bringing Nova along and taking care of her leads to the conclusion that Maurice started the trend of keeping mute humans as a kind of pet, leading to the hunting, caging, and experimentation in the original film. And Maurice would be disgusted to know what his act of kindness eventually wrought.
It's never proven if the mutated virus actually destroys intelligence or not, but even if only takes away the ability to speak, that would mean that with most of human culture gone and/or destroyed, the only way to transmit all knowledge is through speech (assuming that sign language is not taught or apes manipulate known history, like in the original movie) and with that ability gone, future generations of humans won't know anything about their past, culture, and knowledge, which would make the colonel right: The virus actually takes away intelligence from humans, but not the way he thought.
If this is true, then the last scene with the Colonel would suggest that once the Colonel got the virus, he understood that the virus didn't take away intelligence, only speech, which means that all those people he killed died for nothing, and even worse, his son died for nothing, having a complete breakdown and ultimately committing suicide.
All of this can be true because in his last scene, he is actually trying to talk to Caesar. According to one viewer is he saying - "You took John from me. I hate you. I hate you! I want him..." and then when is Caesar aiming at him, he repeats "Do it!" His son's name was John.
If the Colonel's words about every surviving human succumbing to the new virus are to believe, then they becomes even more horrifying for the apes since the Colonel knows he and his troops will get infected one day and as such tries his best to drag the apes down with him out of spite.
