Spoilers for War for the Planet of the Apes.
War for the Planet of the Apes is the epic end of the Apes prequel trilogy, yet it does more than just wrap up the past three movies. Of course, the main story is that of Caesar, Andy Serkis' scientifically-evolved chimpanzee trying to Moses his tribe through a land ravaged by man's self-destruction, but within that there's a lot of major honoring of the fifty-year-old series and some explanation of its biggest ideas that have been carefully dropped throughout the new series.
Indeed, while the Simian Flu, mute humans and Bad Ape may all appear to be random artifacts of a destroyed society and simple cogs of the climactic narrative, together they form an amazing backbone to the personal story at the forefront of the Apes prequels. It's easy to point to the work Serkis has done with directors Rupert Wyatt and Matt Reeves as the emotional core of these films, although perhaps their true brilliance lies in the handling of these secret elements. Let's take a deeper look.
Simian Flu Explained
In Rise, we were introduced to Will Rodman, James Franco's neurologically-focused chemist who was trying to find a cure for his father's Alzheimer's. The first drug, ALZ-112, was successful enough in increasing the brain function of chimp subject Bright Eyes to suggest human trials but was canceled when the ape went berserk trying to protect her child - the future revolutionary Caesar. What's important to note here is that there's nothing to suggest that 112 had negative human side effects; it was used secretly on Will's father, Charles, to initially great effects over the ensuing years. Over time, the Alzheimer's became resistant but Will managed to leverage development of a new version of the drug, which was tested on lifetime lab ape Koba. Caesar later used this when, having been sentenced to a primate shelter, to infect the other apes at the facility teaming up with the subjects in Will's lab and others from San Francisco Zoo to make a bid for Muir Woods.
Ostensibly ALZ-113 is the ape-smartening drug, but unlike 112 it is very dangerous to humans. One of the lab technicians is infected during Koba's experimentation and begins to fall ill, eventually dying - but not before infecting Will's neighbour, a pilot, who quickly spread the virus around the world. Ten years later, when we return to the world in Dawn, the entire planet has been torn apart; most of the population were killed and the survivors who have undefined immunity have been driven primitive under martial law, obsessed by survival, in-fighting, and fear of the ape threat - a threat born of the same virus that led to such a damaged humanity.
In War for the Planet of the Apes, two years later, things get interesting. Just as how ALZ-112 eventually couldn't stop the alzheimer's, ALZ-113 has begun to mutate and affect those immune in a much darker way. Instead of killing them, it reverses the original increasing of brain functions and turns humans into mute, unaware beasts - not a far step from the state of man in the 1968 classic.
In the original Planet of the Apes, before heading along the beach and finding a battered Lady Liberty, Taylor mused "a world where apes evolved from man? There must be an answer." In the middle of the Cold War, that solution was vague but alluded to be our impending nuclear apocalypse. In the 2010s that's not as prominent a threat (relatively), and so it's been updated to reflect our modern fears with scientific experimentation, yet through all the while the same arrogance and hubris is powering it. What War's done, however, is have the specific reason for why Caesar and co. became intelligent also be the explanation for man's fall - it's given a scarily elegant answer to Taylor's musings 49 years previously (or, rather, 2000 years in the future).
But there's another side to the Simian Flu and this connectivity - and it comes from a very unexpected source.