Lightning flashes as a young woman and her infant son are lowered from a burning ship in a small rowboat. Her husband barely manages to escape the flaming ruins of the sinking vessel and reunites with her in the rowboat. As the storm continues, they turn warily towards the dark shadow of land on the horizon.
On the mainland, in the jungles of Africa, a family of gorillas is settling down for the night. Young mother Kala (Glenn Close
) and her mate Kerchak (Lance Henriksen
), the leader of the clan, rest with their baby.
The human family makes it to shore by morning and scope out their surroundings before deciding to build a new life for themselves. They construct a tree house using material from the wreckage while Kerchak and Kala play happily with their baby. Everything seems right until one night, while Kala and Kerchak are sleeping, their baby strays from the nest, chasing a butterfly. The leopard, Sabor, on its nightly prowl, comes upon the baby gorilla which cries out before being swept away. Kala and Kerchak run to the rescue, but arrive too late. Kala, grief-stricken, stays at the rear of the clan as they move to new nesting grounds the next morning. Suddenly, she hears a crying sound and runs through the jungle towards the source. She soon comes upon the tree house the human family had built and cautiously enters the dwelling. The place is in shambles; wind blows through a broken window and a spent shotgun lies on the floor. Kala notices shapes in the corner of the room and sees the outlines of two bodies against the wall. Bloody paw prints are scratched into the floor. Startled, she backs up onto a picture frame showing the faces of the family, including the baby. The cry starts up again and Kala finds the human baby still lying in his crib. They investigate each other for a moment and Kala is overcome with maternal instinct, deciding to adopt the baby. Before she can leave, Sabor, who had been hiding in the rafters, attacks. Kala manages to escape by jumping into the rowboat hanging outside the tree house, leaving Sabor tangled in the mess of ropes.
Kala returns to the gorilla clan and shows her new baby to the other females, who react with confusion. Kerchak is not keen on the idea of Kala keeping a baby that is not of their kind and demands that she take it back. On Kala's fierce insistence, however, he allows her to keep the baby as long as it was alone but refuses to acknowledge it as his son. A young gorilla named Terk (Rosie O'Donnell
) takes a liking to the baby, though she doesn't quite agree with his new name, Tarzan.
Tarzan (Alex D. Linz
) grows into a strong young boy with a penchant for mimicking animal noises, though he has a hard time keeping up with the moving clan. His best friend Terk looks out for him and always makes sure that he stays away from the disapproving eyes of Kerchak, but her friends label Tarzan a 'hairless wonder' and refuse to play with him. Determined to prove himself, Tarzan follows Terk and her friends to a cliff side where, in an attempt to intimidate him back to the clan, Terk instructs him to retrieve an elephant hair as a way of impressing her friends. However, Tarzan takes this ruse seriously and leaps off the cliff, belly-flopping into the water below. He quickly learns to swim and heads towards a herd of bathing elephants. A young and germophobic elephant named Tantor (voiced as adult by Wayne Knight
) mistakes Tarzan for a piranha, despite there being no piranhas in Africa. Tarzan manages to grab onto one of the elephants tails but incites panic on the whole herd who form a stampede and run ashore. Terk's friends are chased back towards the clan and, while no one is hurt in the stampede, Kerchak is forced to rescue a baby gorilla before its trampled. An unconscious Tarzan is pulled ashore by Terk. Tantor, still believing that Tarzan is a piranha, pulls Terk away until Tarzan comes to, revealing a single elephant hair in his hand. Kerchak and the other gorillas arrive and demand to know what started the stampede. Tarzan confesses and tries apologizing to Kerchak who argues Kala's defense to give Tarzan another chance. When Kerchak angrily states that Tarzan will never become one of the clan, Tarzan runs off. Later, he angrily splashes mud onto his face, thinking that it might make him look more 'gorilla'. Kala appears and affectionately shows him that they are actually one and the same; same hands, same eyes, same heart. Filled with a renewed sense of motivation, Tarzan promises to be the best ape ever.
As he grows older, he learns to gain strength and inspiration from other animals of the jungle including creating his first spear after watching a rhino scratch a tree with its horns. Now an adult, Tarzan (Tony Goldwyn
) has become stronger and swifter, managing to travel faster than the gorilla troop by surfing through the trees. During a wrestling match with Terk, the gorilla troop is attacked by Sabor. Kerchak rises to the defense but is overpowered. Seeing this, Tarzan swings in brandishing his spear and engages Sabor in a fierce battle, eventually coming out victorious. He presents the body of Sabor to Kerchak who reacts respectfully to Tarzan. The heartfelt moment is interrupted by a loud noise which encourages the gorillas to move out but arouses Tarzan's curiosity. He soon comes upon a trio of humans consisting of Professor Porter (Nigel Hawthorne
), his daughter Jane (Minnie Driver
), and their guide Clayton (Brian Blessed
). Porter is on an expedition to study gorillas and becomes particularly excited when he stumbles on a nesting site; this proves his theory that gorillas are primarily social creatures that live in family groups. Jane shares his enthusiasm but Clayton remains under the impression that gorillas are wild, savage beasts. Tarzan is nearly discovered by the trigger-happy Clayton before the trio continues on its way. Jane stays behind when she comes across a baby mandrill baboon and whips out a sketchbook to draw him. The baby, taking a fancy to the drawing, steals it and runs off. Jane takes the drawing back from him which makes him cry, attracting the rest of his family, a rather large baboon troop, and they begin to chase Jane. Tarzan, watching all this from above, swings down and rescues Jane before she can fall into a chasm. Tarzan uses his acrobatic skills to navigate the tree tops and elude the baboons, but not before giving the drawing back to the baby.
Tarzan brings Jane to a sheltered spot in the trees and recognizes her as someone like him. He gently holds her hand up to his and listens to her heartbeat, much to her discomfort. His ability to mimic allows him to make vocal contact and they successfully introduce each other. Then, Tarzan carries Jane and swings out of the trees towards Jane's campsite where they heard additional shots from Clayton's gun.
Meanwhile Terk, a small band of gorillas, and Tantor are looking through the jungle for Tarzan. They soon come across the Porters' campsite and begin playing and making music with what they find, creating a large mess in the process. Tarzan and Jane arrive and Jane realizes, as Tarzan and Terk are reunited, that he's one of them. The rest of the gorilla troop arrives at the camp, attracted by all the noise, including an angry Kerchak. He orders the troop, and Tarzan, to leave before Porter and Clayton return. Jane tells them what happened and dreamily mentions how she met Tarzan.
Despite Kerchak's warning that the gorillas must avoid the humans, Tarzan is adamant about continuing to visit them and angrily asks his mother why she didn't tell him there were other creatures like him. Over a period of time he goes back to the camp where Jane and Porter teach him English and all about the human world. After a while, they ask him if he can lead them to where the gorillas are, but Tarzan refuses, remembering how Kerchak felt about the humans. Clayton appears to be the most frustrated by this news. On one return to the camp, Tarzan discovers that more men have arrived and are loading items out of camp and towards a large steamer that is anchored off shore. Jane explains that they are to go home to England and asks Tarzan to go with them. When Tarzan realizes that he won't be able to come back to the jungle, he implores Jane to stay with him. She tearfully says no and runs away. Clayton slyly proposes to Tarzan that Jane will stay longer if she could see the gorillas, so Tarzan agrees to take them.
In order to lead the Porters to the gorilla troop safely, he persuades Terk and Tantor to disguise themselves as the humans and lure Kerchak away. The plan works and Tarzan leads the humans to the troop. Everything appears to go smoothly until Terk and Tantor appear suddenly with Kerchak right behind. When he sees the humans he stops in shock but attacks Clayton when he sees him pointing his gun at another gorilla. Tarzan tackles Kerchak and holds onto him while Jane and the others escape. Tarzan then releases Kerchak, nearly choking him, as the troop watches. Tarzan tries to apologize but Kerchak accuses him of betraying the family. That night, Kala approaches a confused and forlorn Tarzan and takes him to the tree house where she found him. There, Tarzan discovers his true past and finds out who his real mother and father were. Kala advises him that no matter what he decides, he must do what makes him happy. Tarzan decides to leave with Jane and the others, donning a suit that belonged to his father. Before he leaves, however, he tells Kala that no matter where he goes, she will always be his mother.
Tarzan leaves with Jane, her father, and Clayton the next morning, boarding a small dinghy towards the large steamer. Once on board, however, Tarzan is greeted by fierce looking thugs who force Jane and Porter into the hull of the ship. Tarzan attempts to escape, jumping onto a smoke tower, but the smooth metal is difficult for him to hold onto and he crashes to the deck below. Clayton reveals to be more than just a jungle guide; he intends to capture the gorillas and sell them for a hefty profit. Outraged by Clayton's betrayal and his own naivety, Tarzan lets out a yell which reaches the ears of Terk and Tantor. Already angry about Tarzan leaving, Terk is cynical to Tantor's statement that Tarzan could be in trouble. Showing a surprisingly assertive side to himself, Tantor grabs Terk and plunges into the ocean towards the steamer as Clayton and his thugs take a small boat inland. Tantor and Terk overcome the guards on the boat and release Tarzan and the others.
As night falls on the gorilla family, a flare lights up the sky in red and the gorillas are overwhelmed by Clayton's gang. Many gorillas are tied up and put into cages, but Kerchak breaks through his ropes. Clayton strings him down again and claims that the silverback would be better off stuffed. Before Clayton can shoot, Tarzan lets out a loud battle cry, leading other animals of the jungle into the clearing, and frees Kerchak. Kerchak is amazed that Tarzan came back, to which Tarzan replies, "I came home." Jane and Porter arrive on Tantor and even the mandrill baboons, led by the baby, enter the fray. As Tarzan and Jane release Kala from her cage, Tarzan's arm is grazed by one of Clayton's bullets. Seeing this, Kerchak rushes at Clayton but is shot. Tarzan charges angrily at Clayton but is forced to run and hide as Clayton fires multiple shots at him. They both climb into the canopy and begin to fight on the tree branches. Tarzan wrestles Clayton's gun from him and points it at him, but hesitates. Clayton laughs and taunts Tarzan to become a man and shoot him. Tarzan mimics a gunshot, startling Clayton, before smashing the gun to pieces saying, "I'm not a man like you." Clayton brandishes a machete and swings it at Tarzan, forcing him to fall back. He catches onto some vines and backs into the trunk of a tree. Clayton follows but Tarzan brings down a nest of vines, entangling him. Clayton slashes blindly at the vines around him, not realizing that one is wrapping around his neck. Tarzan tries to stop him, but with one last swing, Clayton cuts the vines they were holding and they both fall. Tarzan lands safely on the ground, but Clayton is hanged.
Tarzan returns to the troop to find Kerchak dying and asks for his forgiveness. Kerchak tells him that he was mistaken about Tarzan; that he had always been part of the family and must now lead them in Kerchak's stead. Kerchak then puts his hand on Tarzan's shoulder and calls him son for the first time before he dies. Tarzan then stands before the rest of the gorilla family as their new leader and leads them into the jungle.
The following morning, Jane and her father say farewell to Tarzan as they leave shore in the dingy bound for the steamer. Tarzan waves goodbye from the shore but Jane is too heartbroken to return the gesture. Porter notices how sad his daughter is and encourages her to follow her heart and go back to Tarzan. Jane jumps excitedly into the water and runs into Tarzan's arms, kissing him. Porter follows, telling the captain rowing the boat to say that they were never found. "After all, people get lost in the jungle every day."
The rest of the gorilla troop arrives on the beach, smiling as Tarzan and Jane kiss. Jane tells the gorillas, in the language taught by Tarzan, that she is staying. They all cheer and Tarzan, Jane, and Porter live happily together in the jungle.