Caesar works the system and gains the respect of the other monkey inmates. First he pickpockets a bottle opener and makes an extended arm from twigs to open his cell. He unleashes the huge gorilla, and then takes the popular monkey outside away from the others to frighten the little life out of him.
With free reign of the sanctuary he plots his escape with big Red, his signing friend, Shawshank style - just without any posters of a hairy Rita Hayworth.
Soon Will's father's health deteriorates and he dies in his sleep. Will is forced to proceed with experiments on the new drug against his wishes, but while experimenting on an evil looking monkey his lab assistant's mask is knocked off, and he inhales the gas. Will finally quits, while the lab assistant (who looks like Alan from The Hangover, isn't doing so well either).
Will finally realizes that he cannot beat the system so offers a bribe to John Landon (Brian Cox) to let Caesar leave. However Caesar is enjoying his new alpha-male role and his plan is coming together nicely - and doesn't want to leave the others. Will leaves, dejected. And poorer.
Caesar decides to call round Will's house - and finds a few drug canisters in the fridge. He returns to the sanctuary, pops them open, then rolls them down the corridors so his new friends can grow a little smarter.
The next day they all have a group seminar in the play area, to the amazement of the guards. That night Caesar refuses to go back to his cage and squares off against Dodge, the bad human. We then have the ridiculous line -- "Get your stinking paws off me...", before Caesar speaks for the first time. Soon Dodgy stands before the apes with his stun gun ... until Caesar turns on the hosepipe. Dodge dies from electrical burns.
The monkeys escape. And even though there were just about 30 of them on the inside, suddenly their number has picked up to over a hundred.
About this time, the bearded lab tech tries to call round to warn Will and sneezes all over his neighbor -- surely the most unluckiest neighbor around. The lab assistant soon dies in his apartment from serious flu-like virus syptoms.
Will calls round the sanctuary the next day to see the carnage. The monkeys head towards the lab and free their friends -- usually only held 10 at a time we're told, but now their total number has somehow swollen to over about 300 chimps.
They are heading towards the Golden Gate Bridge. The police set up a road block and have orders to take them out. The apes push through, with some swinging from the wires while Red takes his group under the road, and then crash down on the cops. A chopper holding the lab boss tries to take out Caesar, but the big Gorilla gets in the way to take the bullets. He then jumps onto the chopper, causing it to crash on the bridge.
Caesar comforts his dying friend, then kicks the chopper off the bridge when the lab boss asks for help.
They continue on their journey to the old oak trees. Will follows and asks Caesar if he would join him and go home -- but Caesar whispers in his ear that "Caesar is home".
As it ends, the unlucky neighbor turns out to be a pilot and gets ready for work. As he reaches the airport, he realizes he has a little sniffle. The end credits show how the virus could spread out from that airport to affect the world population in a few days.