Will Rodman, a scientist at the San Francisco biotech company Gen-Sys, is testing the viral-based drug ALZ-112 on chimpanzees to find a cure for Alzheimer's disease. ALZ-112 is given to a chimp named Bright Eyes, greatly increasing her intelligence. However, during Will's presentation for the drug, Bright Eyes is forced from her cage, goes on a rampage, and is killed. Will's boss Steven Jacobs terminates the project and orders the chimps euthanized. However, Will's assistant Robert Franklin discovers that Bright Eyes had recently given birth to an infant chimp. Will agrees to take in the chimp, who is named Caesar. Will learns that Caesar has inherited his mother's intelligence and decides to raise him. Three years later, Will introduces Caesar to the redwood forest at Muir Woods National Monument. Meanwhile, Will treats his dementia-suffering father Charles with ALZ-112, which seems to restore his cognitive ability.
When Caesar reaches adolescence and sees a dog on a leash like his own, he questions his identity and learns of his origins from Will. Meanwhile, Charles's condition returns as his Alzheimer's becomes resistant to ALZ-112. Caesar injures a neighbor, Douglas Hunsiker, while defending a confused Charles. As a result, he is placed in a primate shelter where he is treated cruelly by the other chimps and the chief guard, Dodge Landon. Caesar learns how to unlock his cage, gaining free access to the common area. With the assistance of a gorilla named Buck, he confronts the sanctuary's alpha chimp named Rocket and claims that position. Meanwhile, Jacobs clears development of a more powerful, gaseous version of the drug   ALZ-113   when Will tells him it can not only heal brain diseases but also improve intelligence. Will takes the drug home to try to save his father, but Charles declines further treatment and dies overnight.
After attempting to test the drug on a scarred bonobo test subject named Koba, Franklin becomes exposed to ALZ-113 and becomes ill. Attempting to warn Will at his home, he sneezes blood onto Hunsiker and is later discovered dead. Will attempts to reclaim Caesar, but the chimp refuses to go home with him. Instead, he escapes from the facility and returns to Will's house, where he takes canisters of the ALZ-113. Upon returning, Caesar releases the gas and allows it to enhance the intelligence of the other apes. When Dodge attempts to get him back into his cage, Caesar shocks him by speaking for the first time, yelling "No!" Caesar then electrocutes the cattle prod-wielding Dodge by spraying him with water, unintentionally killing him. The apes flee the facility, release the remaining chimps from Gen-Sys, and free more apes from the San Francisco Zoo.
A battle ensues as the ape army fights their way past a police blockade on the Golden Gate Bridge to escape into the redwood forest. Buck sacrifices himself to save Caesar by jumping onto the helicopter in which Jacobs is riding. The helicopter crashes onto the bridge, trapping Jacobs in the wreckage. Jacobs is then killed by Koba. As the apes find their way into the forest, Will arrives and warns Caesar that the humans will hunt them down, and begs him to return home. In response, Caesar hugs him and says that, "Caesar is home." Will, realizing that this is indeed their last goodbye, respects Caesar's wishes. In a mid-credits scene, an infected Hunsiker leaves his house for work as an airline pilot, arriving at San Francisco International Airport for his flight to Paris. His nose begins to drip blood onto the floor. A graphic traces the spread of the humanity-ravaging virus around the globe via international flight routes.
Output: Who kills Jacobs?