Pope's past comes to light as his ascension from commanded to commander stirs trouble among the apes. With no sign of Pope's return, Koba must do away with their kinship for the honor of Caesar. Alexander has been taken. Rita is dying as the simian flu takes more of her every day. The hardest days of Malcolm's life are upon him and there is nothing he can do that will make things right. Nothing to do but try.
Cora and Fifer conceal themselves in a tree, observing two gorillas from their troops guarding the zoo entrance for Pope. Cora believes escaping is too risky, but Fifer believes not warning Caesar of Pope’s coup is more dangerous. He tells her to stay to keep an eye on Pope and jumps down, knocking one of the gorillas off his horse. The other gorilla thrusts his spear into Fifer’s back, forcing Cora to jump and intercept the gorilla, shouting at Fifer to leave. The gorilla pins her to the ground.
Back at Ape Village, Maurice teaches a group of apes that their strength comes from unity. One chimp asks if Caesar’s strong alone, can apes be strong alone. Maurice attempts to explain, but Caesar appears, stating he is strong, but only as a family with his fellow apes. The lesson is interrupted by ape guards sounding an alarm. Rocket tells Caesar that Fifer has returned wounded and Koba is with him. The wounded Fifer recalls what has happen during the expedition of what Pope has done and his threat to Caesar.
Back at the zoo, Pope’s group begins to train the primal apes in the artic exhibit. One primal chimp lunges at one of Pope’s chimp, only to get punched in the gut. Enraged, Pope orders them to do the exercise again. Pope’s second in command, Rex, approaches, telling Pope Cora has been captured but isn’t cooperating. Pope states they know where Fifer went and orders him to bring her, to see if she can be swayed. The beaten Cora is brought to Pope, shivering in a cold puddle, refusing to answer Pope. Seeing she can’t be swayed, Pope gives the word to his apes, opening a steel door to reveal a savage polar bear. The bear lunges at Cora.
At the entrance, Rex wonders if Caesar will come. Pope disagrees, claiming Caesar’s too proud. He theorizes that Caesar would send Maurice to parley or Koba for war. He was about to tell Rex to prepare his troops until a primal chimp approaches them, touching Pope. Pope lifts the ape in anger, shouting to never touch it until Rex spotted their scouts. The scout leader, Bon, tells Pope they found something.
As Pope and Bon sit by a campfire, Bon tells him they’ve found large groups of humans while looking for Fifer. Pope believes the humans are a threat, forcing him to send another scouting group to find the humans. He turns to the fire, stating that humans will be apes’ slaves, then Caesar.
Caesar, Maurice, Koba and Rocket counsel on Pope’s threat in a secret part of the village. Maurice states Pope knows nothing of building a world, only chaos and destruction. Rocket wonders if Pope is a danger to them since he’s far away, which make Caesar believe if Pope will act on his threat. Koba believes he will, considering he has already turned the apes in his troop against Caesar. Maurice implies it would be best to let Pope go, only for Koba to remind him of Pope’s act of making primal apes his slave. Koba believes Pope is just like the humans. Caesar agrees with Koba and states apes are not free to make the primal apes their servants. He orders Koba to gather a group of apes to head into the city with an offer of peace. Rocket attempts to join Koba, but Caesar tells him to stay in the village with his newborn son. As Rocket and Maurice left, Caesar calls to Koba, telling him Pope will never surrender and as long as he lives, every ape within the village will be on constant alert for Pope if he’s banished. Understanding what Caesar’s implying, Koba agrees to kill Pope.
Back at the compound, Malcolm and Rita remain in shock from Alexander’s abduction. Rita reminds Malcolm of the oath they made to protect their son, even if it means sacrificing one of their lives. Malcolm agrees, but ponders on what will happen after they rescue Alexander, which Rita states it’s not important. Malcolm becomes dismay by his wife’s response and claim she has nothing to lose until he succumbs. Taking her hand he agrees to help her find Alex.
In a tent, Shavers and Amber discuss where the marauders are heading until Malcolm and Rita barge in. Malcolm agrees to become Shavers’ engineer, only if he helps him and his wife find Alexander. Shavers told them they’ve located the boy and the other abductees on a barge near a lake, but they need time to gather the resources they need for a rescue mission. This upsets Malcolm and Rita, who believes by then, it would be too late. Shavers remind them the reality of this situation: they are dealing with a rogue group who are forcefully taking people and bartering them. Angered, Rita demands the location of the barge and Malcolm will join the project Shavers offered. Amber is hesitant, but Malcolm states he’ll come up with a plan by night and asks for them to be prepared. Shavers agree, but he asks Malcolm is he has his word. Malcolm states if they help him rescue his son, he’ll give his word.
At night, Malcolm, Rita, Shavers and Amber reached the barge. Amber spots one guard standing by a speedboat, sneaks up behind and quickly incapacitates him. Malcolm hops on the boat, stating the marauders will notice the boat’s engine once it’s turned on. As Shavers unties the boat’s rope securing it to the docks, he questions the plan. Malcolm assures him it’ll work, messes with the chemicals in the engine and hot-wires it. As Rita pulls Malcolm off the boat, he pushes the throttle lever to make it move. However, the boat explodes early.
They managed to sneak in the barge, but the lieutenant states they should leave now, but Rita says they’re not leaving Alexander behind. Malcolm hears a hollow thud underneath his foot and investigates, realizing the panel can move, revealing a hidden storage compartment. Malcolm asks how many of Shavers’ people were taken and he states three were abducted with Alexander. Rita revealed to Shavers what was in the compartment: people tied down. As Malcolm plans to head down the compartment, they all hear a noise. Amber told them that was the barge’s engine, and the ship begins to move.