As Caesar learns the value of sacrificing a few for the many, Koba will be forced to confront Pope and his militia of apes. On the other side of the world, with his son kidnapped and wife fading with every hour, Malcolm has one chance to make things right before it all comes crashing down around him.
Koba’s troop moves swiftly and silently through the ruins of San Francisco. They stop on a rooftop near a prison building with a few apes from Pope’s troop. One chimp asks Koba if they should attack now, but Koba told him not to as he surmise Pope is keeping something in the building and tells his troop he’s going inside to see what Pope has that’s important.
Using the power lines, Koba sneaks onto the police station’s roof and sneaks inside. He reaches a dark and flicks the light switch and was shocked by what he saw: humans in prison cells. He examines the beaten and starved humans, begging for mercy. One of the them pleads with Koba to free them, but Koba turns back to where he came from and flicks off the lights, leaving the humans in the cells.
In the center of the zoo, Pope declares, clad in tribal war paint, declare his army with the primal apes and humans watching from the cages. Pope turns to Rex, telling they must prepare for an invasion until Rex spotted Koba and a troop heading for them. Pope turns, seeing that Caesar has declared war on him. With both troops in a standoff, Pope berates Koba as a tool of Caesar, but Koba states Pope is acting like a human. Pope ignores the comment and declares himself a true leader, making apes strong while believing Caesar makes them cowards. Koba tells Pope that apes are not free to make slaves of their own kind and cites Caesar’s philosophy: apes together, strong. Pope pulls his chimp by his leash, stating he’ll only enslave primal apes, which he calls stupid animals. Enraged by what he was called by humans, Koba makes the first move and both troops charge at one another.
In the barge, Rita assures one of the captives, a member of Shavers’ group, they won’t harm them. She removes the blindfold, but places her hand on his gagged mouth to keep him quiet. She asks him if he spotted a twelve year old boy before removing the gag. He pleads with Malcolm and Rita to get him and his fellow prisoners out of the barge, but Malcolm assures him they will after they find their son. The man tells them the marauders took the kids to a different place up top until they notice key noises. Rita and Malcolm hid as the door unlocks and one of the marauders, a woman, comes in the room, making a threat to the prisoners to not do anything stupid.
She notices the ungagged man and points her gun at him. As she places the gun’s end on his head, Malcolm appears behind the marauder, pointing his gun at her and telling her to drop her weapon. She lowers her gun, but catches Malcolm off guard with a spin kick to his maimed leg. She attempts to reach her firearm, but Rita stands above her with a gun pointing at her head. She demands to know where the children are, but the marauder doesn’t comply, forcing Rita to make her look at her face. The marauder concedes to Rita’s fury, telling them the children are kept on the deck. As Malcolm knocks her out, Rita tells him to tie and gag the marauder while she cuts the captives loose.
On one side of the boat, a marauder looks out to sea while he smokes. He turns by a loud noise and mistakes it for the boat falling apart until the door knob turns and the captives emerge, one of them wielding a pipe. Before the marauder could make a move, the captives gang up on him and bludgeoned him before tossing him overboard. On the other side, two marauders ready their rifles and head for the freed captives. Malcolm and Rita appear around the corner, Rita wondering if Shavers and Amber will keep their end of the deal, but Malcolm believes they abandon them. Rita tells Malcolm to not be cynical and be the man she married: a man with hope. She climbs up the ladder to the upper deck and spots two guards by two containers. She lowers herself back down and tells Malcolm she’s found the kids.
Preparing herself, Rita climbs all the way up the ladder and pretends to be beaten, wiping the blood coming from her nose. While the guards question her, Malcolm sneaks from behind and pries one of the containers open, spotting a little girl and telling her to remain quiet while she sneaks out of the deck. Realizing her plan’s falling apart when the guards asked for her name, Rita pulls out her gun and kills both guards. Malcolm rushes to her, but Rita assures him she’s fine and asks where Alexander was until her appears and runs to her. Rita calms him down and assures him everything will be okay until Malcolm points out they have no way to leave the boat. They hear gunfire and run towards it, seeing Shavers and Amber in a life boat, trading fire with the marauders.
Shavers continue to shoot as he tells the captives to get on the life boat. Rita, Alexander, Malcolm and the girl run for the boat while Malcolm spots a marauder and shoots at him. Shavers turns to one of his people and tells him they can’t wait anymore. A marauder lies up his gun at Amber and prepares to fire until Malcolm kicks him in the head. Rita screams out Shavers’ name, who was surprised to see them still alive. Malcolm, Rita, Alexander and the girl climb down onto the boat, leaving the barge with only a handful of freed captives. Malcolm and Shavers are upset for leaving the rest of the captives behind, with Shavers complimenting on Malcolm’s compassion.
As they wade to shore, Alexander asks Malcolm if they’re going home until Rita stops him and tells him they need to talk.