Now, I'm no medical expert but after seeing that humanity is doomed and likely to be wiped out by the virus I wondered... there were still humans in the Planet of the Apes, being hunted, right? Sure the humans were a bit slow, but what are they? Immune? Then I realized... the virus was meant to cure Alzheimers, and the human it was tested on was cured, only to soon revert. Medicines given to someone without a disease can cause problems or issues. So one might say that the disease is only fatal to regular humans, while those suffering from Alzheimers get cured for a time before reverting to their simple, more forgetful selves.
Trouble is, people with Alzheimers are usually too elderly to breed, meaning they're unlikely to be the ancestors of whatever future generations of intellectually-stunted humans remain. More likely, the plague will fall shy of a 100% mortality rate, but will leave any lucky survivors quite mentally damaged, and their children too.
The sequel says that the virus had a 99.8% mortality rate.
And the third film has the revelation that whoever was lucky enough to survive the first pandemic is now at risk of catching the second strain that does cause mental regression (or at least a simple loss of speech).
The apes from the zoo were unexposed to ALZ unlike the shelter apes and the lab apes. That meant that during the bridge scene some of the more flighty and disorganized apes were still just of regular intelligence, and only later became smarter once they mingled with the enhanced apes in Muir Woods and were infected with the virus too.
The final scene of the film where Koba wanted to kill Will for being a human (and one of the scientists of the company that experimented on him) and Caesar defending the latter perfectly foreshadowed the entire plot of the sequel.
Before running away, Bright Eyes tries to jump back into her cage. This act seems meaningless and is entirely forgetable if you don't rewatch, when you know baby Caesar is inside the cage.
The last scene fades out on New York, the location of the original film. The credits reveal that the plane's destination is Paris, the origin of the astronauts in the novel.
The war tactics used by Caesar in the bridge aren't the result of the drug. Real-life chimpanzees are known for using guerrilla-like tactics to expand their territories (the Gombe Chimpazee War), the drug is only enhancing what's already there.
What do you think Will's neighbor probably did before he left on his flight at the end of the movie? Hugged his children. So much for Improbable Infant Survival.
Remember when Will was about to give his father the new ALZ-113 drug to permanently cure him of Alzheimer's but his father refuses it, prompting him to let him go. Later in the film, it's revealed that the drug is fatal to humans. If Will's father didn't refuse the drug at the last minute nor if Will didn't listened, he could have died a long painful death.
And Will would have been next.
Then again, they would have had an earlier warning about the fatal side effects of the drug, and maybe could have prevented the pandemic. . .
Even if Franklin hadn't come across Hunsiker, he would have probably infected many other people he met after falling ill, including Will himself. Who would say that some of them wouldn't travel by bus, plane, ship or train? The second Franklin inhaled the gas and left the Gen-Sys facility (or for that matter, the room he was infected in), the whole world was doomed to crumble down.
The interquel novel Dawn of the Planet of the Apes: Firestorm has one of the protagonists investigate Will's house during the subsequent Simian Flu outbreak, only to find Will and Caroline missing and the computer equipment confiscated by a third party. Then he meets with Linda Anderson's sister and witnesses her being shot by a Gen-Sys hitman, only surviving not for long) thanks to another citizen taking the man out in a Mutual Kill. This brings up a question on whether Will might have died from Simian Flu... or could he have been silenced by the very company he used to work for in a haste coverup attempt.
Koba is probably the most vicious ape in the story, particularly toward his captors. When you realize that bonobos are one of the least aggressive species of ape (they'll fight if threatened, but they're nowhere near as psycho as chimpanzees), it makes you wonder: What were those scientists doing to him?
It wasn’t actually the scientists, at least not completely. The “Dawn” prequel book explains it all. He saw his mother die at the hands of a drunk man and was then sold to a human who beat him, electrocuted him, forced him to do silly tricks, slashed his face with a knife and blinded his left eye by burning it with a lit cigarette. Then he ended up in the lab undergoing all kinds of painful experiments and otherwise kept in complete isolation. Still a horrific life to live, and could still possibly turn a bonobo completely crazy.
The fact that Koba was the one who exposed Franklin to the virus. Koba is entirely responsible for everything that went down in the sequel...and then more.
