The apes of Simian gather in their ancestral tree to welcome the birth of two sons to the King of Apes. King Simeon rules over dozens of apes in an old tree somewhere in the Savannah desert. Vladimir, the king’s faithful advisor, lets the king know there is a problem. Apparently, the queen had given birth to two sons instead of one. The first monkey prince is so tiny and weak, but the second monkey is strong and healthy looking. Since the tiny monkey came out first, he is the direct heir to the throne. The monkey witch arrives and advises the king to get rid of the tiny price as he is a bad omen. She says he is a mistake by nature, and the apes will never accept him as their prince. The king yields and hands the baby to Vladimir to do away with the monkey while the queen sleeps.
The queen looks for her babies when she wakes up and makes the king promise that he will take care of them for her. She dies after that. King Simeon introduces the crown prince—Vanya, the strong and healthy monkey—to the apes of the kingdom. Vladimir takes the weak monkey to a cliff to throw it into the mouth of the wolf. The child clings to Vladimir’s hands, causing him to have a change of heart for a moment. However, Vladimir’s allegiance lies with the king, so he throws the monkey and walks away. Meanwhile, the weak monkey didn’t fall directly into the mouth of the wolf but was hanging on a vine. The wolf finally snaps the baby off the vine and bites one of its hands. Before the wolf can do total damage to the baby, a proboscis monkey saves it.
The baby is unable to walk like an ape because its right arm has been ruined by the wolf’s bite, so its saviour, who is called Ian, allows him to ride on his back. The weak monkey is now an adult ape named Edward. He still rides on Ian’s back because one arm no longer works. The arm remains in his loincloth all through the movie. They are good friends who get along, bickering and looking out for each other. They leave far from the other apes. Ian has a speech problem, so he cannot communicate properly. In their little shed, Edward is looking for some figs he kept in a hole covered by leaves. He asks Ian for it, but the ape claims ignorance and an argument starts. Edward finds a mouse and realises that the mouse ate his fi. He starts to pursue it around but cannot catch it with one arm. He discovers the tree sap and plans to use it as a trap for the mouse, but horn sounds distract him.
The horn announces the beginning of coco ball, a sport Ian and Edward love. Ian is reluctant to go since the two are often discriminated against by the other apes. Edward convinces him to go, and they settle in a branch to watch the games. The apes hanging from vines toss the ball around, aiming for a goal shot into the mouth of a skull. The ball is a coconut fruit. Vanya is the first to score and is applauded by the crowd. Another match begins but gets interrupted when Ian tries to catch the ball but ends up falling headlong with it and throwing off the plates from their vines in the process. The ball bounces off and falls into a hole. The pirates get pissed and surround Ian to beat him up, but Edward thinks of something fast. He uses tree sap to get the ball out. The awed primates gather around Edward, asking how he did the magic, but Vanya shows up and takes the ball from Edward.
Vanya tries to throw the ball, but his hand is stuck on it by the tree sap. The other primates try to get him off it, but they also get stuck. The chaos ends when the ball flies out of their hands and lands on King Simeon’s head. Vladimir tries to get it off but pulls a tuft of hair in the process. The king wants to know the culprit but gets tossed around by Vladimir and his cousin, Sergey. The witch noticed Edward and ass Vladimir if he disposed of the child as asked. Vladimir confirms that he did throw the child away. She threatens him and sends him off to find a solution. However, Vanya overhead their discussion and confronts his father about the possibility of another ape taking the throne from him. King Simeon promises to do something about it.
Edward and Ian are in their nest arguing about the white mountains Ian always dreams about when Sergey and Marcel show up on the king’s orders. They tell Edward that he has been summoned by the king. In the King’s presence, Edward is accused of practising magic and explains once again that it is not magic but a few tricks he discovered. He proceeds to show some of those tricks to the king. He makes a crown from leaves and makes a mirror by pouring water into a leaf. The king can see his reflection for the first time and is awed by his facial features. Edward makes a swing for the king and keeps talking to him. They are suddenly attacked by a swarm of insects summoned by the witch. King Simeon is thrown off the swing, and Edward is accused of attempted murder by the witch. Vanya orders for him to be thrown off the cliff, and Ian can do nothing but watch.
King Simeon climbs up and demands to know who threw Edward off the cliff. Vanya says he tried to kill him, but King Simeon accuses Vanya of killing another Simian. Edward wakes up to discover he was thrown off the tree. Ian is hanging from a vine, but it is too high for Edward to reach. He leaves Ian and wanders into the desert. He sees two giant ostriches and tries to grab a bunch of grapes dangling from one ostrich’s mouth. In the process, he learns to stand on two feet like them. A pack of wolves appear, and the trio have to run. Edward first runs backwards but notices the way the ostriches run. He starts running forward and is happy that he can now move fast. His one arm will no longer be a hindrance to him. The other monkeys see him running and cheer him on. The trio run into a field filled with rhinos and make it past them until the rhinos see the wolves coming and start running.
Now Edward is running from the rhinos and the wolves. Edward reaches the end of the path, and the rhinos start to roll like armadillos. Seeing that Edward is about to be crushed by those rhinos, King Simeon jumps in and tries to save him. He fights off some armadillos but jumps in front of Edward when he sees that he is about to be crushed. The chaos dies down, and King Simeon is badly injured from the fight. Vanya comes close to them with a vine to help Simeon back up. King Simeon tells Edward that he is his father before he dies. Vanya takes Simeon’s body away and tells Edward not to even consider themselves brothers. Vanya is crowned king, and he dismisses Vladimir for failing in his duty to get rid of Edward. Sergey takes over Vladimir’s work, and the time for Vanya to choose a bride arrives.
Instead of taking a wife, Vanya makes a declaration that all the apes will be at his disposal, and he has absolute command over all of them. A storm starts and Vladimir is rejected by all the apes. The storm becomes violent, and a tornado appears. Edward discovers Lucie in the tornado and falls in love with her. He chases after her and they become friends. Edward teaches her to stand on two feet, and they discover fire from a volcano. Excited, Edward takes a piece of the fire back to the apes and talks about it. They do not welcome him and stone him on the orders of Vanya. Edward leaves with Lucie, disappointed. He chases a wolf away from its hideout with the fire and settles into the cave with Lucie. The other apes watch Lucie and Edward learn to catch fruit and kill rabbits and other small animals. Edward has also learnt to control the wolf.
The apes leave Vanya and the ancestral tree when they can no longer bear the hunger. The witch summons the tree spirit to frighten the apes, but a young ape—Diego—decides to follow the sound, and they discover that there is no spirit of the tree. It has all been the witch. She tries to eliminate him, but he is saved and reveals the truth. The apes leave the tree and head to Edward and Lucie’s cave. Gizella, a female ape who has always loved Vanya, decides to stay back. Lucie does not welcome the apes after what they did to her and Edward. The apes talk to Edward and make him intercede on their behalf. The apes promise to only eat and go, so Lucie lets them in.
They eat, and they don’t go. They have a party in the cave that night, and Vanya and Gizella watch with sad faces. They continue to watch for months as the apes build themselves a new village. Lucie and Edward are married and expecting a son. They decide to name the child after Edward’s friend—Ian. Meanwhile, the witch has been plotting revenge on the apes for abandoning the ancestral tree. Lucie rests at home while Edward helps the rest of the village with the construction work. All the apes now work on two feet like Edward. They can now hunt for their own food, and Diego can draw realistic images. An argument arises between Sergey and new primates who are looking for shelter. Sergey says there’s no shelter and banishes them. Edward tries to pacify them, and while he does that, a locust invades the village and destroys everything they’ve been working on.
Sergey and the apes are convinced that the witch is responsible for the mess so they go after her. Lucie tells Edward to save Vanya before the mob gets to the tree. Edward calls for Vanya, but he doesn’t respond. The mob arrives at the tree, and Vanya comes out of hiding. The apes promise to let him go if he gives them the tree, but he promises to let them go alive if they leave on their own. Gizella tries to defend the king, but Sergey orders the apes to beat Vanya. Vanya fights back, but he is overpowered. Edward is also stopped from interfering. Sergey orders the apes to cut open the tree and set it on fire. Edward saves Gizella before the tree blows up. However, he is trapped under a burning branch. He calls out to Vanya, who yields and helps Edward. The two run away before the trees blow up. The witch remains in the tree and dies with it.
When they come around, the whole area is filled with smoke. The tree is utterly burnt, and there’s nothing left for the apes. Vanya and Edward end their differences and reveal their relationship to the apes. Sergey tries to cause panic among the apes, but Edward, with Vanya’s help, calls the apes to order. He tells them that there’s hope for them and talks about the world beyond the white mountains. The apes follow the birds to the white mountains, and they discover a world filled with green trees, water and huge mountains. The apes are overjoyed. Edward sees Ian again. Lucie watches the two friends dance around and smiles. The end.