Komplex And The Evil Toad Empire Is Planning To Make An Invasion of Full Scale In The Jungle Depths of The Africa Exterminating An Entire Population of Gorillas For His Sinister Purposes Now The Fate of The African Jungle's Sanctuary It's In The Hands of Dave Felis Brave Team Leader of The T.U.F.F.C.A.T.S. Now He And And The Squadron They're Going To Need more Help Against Komplex's New Jungle Menace And It's To Make Forces With Komplex's Old Enemy And Brave Captain of The Righteous Indignation Crew of The Aniverse And Citizen of Planet Warren Captain Bucky O' Hare and his brave crew: Mysterious Jenny The Aldebaran Cat, Four Armed Ex Space Pirate Deadeye Duck, Bruiser The Beetleguseian Berserker Baboon, Android First Class Blinky, And Earth Boy Genius Willy DuWitt, And also They're Going To Discover The Legend of The Ape Man Tarzan

Meanwhile off the coast of Africa, a married couple and their infant son escape a burning ship, ending up on land near uncharted rainforests (presumably West Africa). The couple craft themselves a treehouse from their ship's wreckage, but are subsequently killed by Dave's former brother turned leopard Sabor, a rogue Seijuujin leopard, former loyal guard of Planet Mugen until he violated the law of not killing Seijuujins and banished in his pre-evolved form. Kala (Glenn Close), a gorilla whose own son was killed and eaten by the vicious leopard, hears the cries of the orphaned infant, and finds him in the ruined treehouse where the parents' dead bodies lie in a dark corner. Kala takes an instant liking to the baby. Kala is attacked by Sabor, who wants to kill and eat the baby, but Kala manages to get him tangled in the ropes holding the derelict rowboat, and she and the baby escape.

The kindly Kala takes the baby back to the gorilla troop to raise as her own, despite her mate Kerchak's (Lance Henriksen) disapproval. Kala raises the human child, naming him Tarzan (Alex D. Linz as a young boy, Tony Goldwyn as a young adult). Though he befriends other gorillas in the troop and other animals, including the young female gorilla Terk (Rosie O'Donnell) and the paranoid male elephant Tantor (Wayne Knight), Tarzan finds himself unable to keep up with them, and takes great efforts to improve himself. As a young man, Tarzan is able to kill Sabor with his crude spear and protect the troop, earning Kerchak's reluctant respect.

The gorilla troop's peaceful life is interrupted by the arrival of a team of human explorers from England, consisting of Professor Porter (Nigel Hawthorne), his daughter Jane (Minnie Driver) and their hunter-guide Clayton (Brian Blessed). Jane is accidentally separated from the group and chased by a pack of baboons. Tarzan saves her from the baboons, and recognizes that she is the same as he is, a human. Jane leads Tarzan back to the explorers' camp, where both Porter and Clayton take great interest in him—the former in terms of scientific progress while the latter hoping to have Tarzan lead him to the gorillas so that he can capture them and return with them to England. Despite Kerchak's warnings to be wary of the humans, Tarzan continues to return to the camp and be taught by Porter, Clayton, and Jane to speak English and learn of the human world, and he and Jane begin to fall in love. However, they are having a hard time convincing Tarzan to lead him to the gorillas, due to Tarzan's fear for their safety from the threat of Kerchak.

When the explorers' boat returns to pick them up, Clayton persuades Tarzan that if he shows the group the gorillas, then Jane will stay with him. Tarzan agrees and leads the party to the gorilla troop's home, while Terk and Tantor lure Kerchak away to avoid having him attack the humans. Porter and Jane are excited to meet and mingle with the gorillas, but Kerchak returns and threatens to kill them after witnessing Clayton threatening some gorillas with his rifle. Kerchak heads directly towards Clayton but Tarzan is forced to hold Kerchak at bay while the humans escape, and then leaves the troop himself, alienated by his actions. Kala reluctantly takes Tarzan back to the treehouse where she found him as a baby, and shows him his true past.

Encouraged by Kala to follow his heart, Tarzan decides to leave with Jane, Clayton, and Professor Porter after saying a tearful goodbye to his adopted mother. When they return to the ship, they are all ambushed by Komplex's Men Decimator, Toadborg And A Group of pirates and it is then revealed that Clayton desires to capture and sell the gorillas in England for a fine price and sell our heroes to Komplex. Tarzan and the others are then locked up in the hull of the ship (however, our heroic T.U.F.F.C.A.T.S. used Stunt Double Jutsu and had excaped), but are rescued by the T.U.F.F.C.A.T.S., Terk and Tantor and race back to the gorilla home.

Decimator, Toadborg, Clayton and his men arrive back in the jungle and capture the gorillas. Making their way back to the gorillas' home, Dave, Bucky, Tarzan recruits some miscellaneous animal friends (baboons, rhinos etc.) And Bucky Calls The Reinforcments of Commander Dogstar While Dave Contacts The T.U.F.F.C.A.T.S. Military Army , and together they fight and/or scare away the rest of Toadborg & Clayton's men, imprisoning them in the very same cages they planned to imprison the gorillas in. As the rest of the gorillas (including Kala) are freed by Jane, Professor Porter, Terk and Tantor, Kerchak and Tarzan together battle Clayton; Kerchak is fatally shot, while Clayton chases Tarzan into the vine-covered trees, where Tarzan gets the drop on him, destroying Clayton's gun. Clayton pulls out a machete, in his haste to kill Tarzan, ignoring his warning about the vine wrapped around his neck. Once Clayton cuts the vine holding him up, he and Tarzan fall, but while Tarzan lands safely, Clayton is killed when the vine snaps his neck, leaving him hanged. Kerchak, in his dying breath, accepts Tarzan as his own adopted son finally, and names him the leader of the gorilla troop.

The next day, as Porter and Jane prepare to leave on a row boat, Tarzan reveals that he now plans to stay with the gorilla troop to continue his position as their new leader. As the ship leaves shore, Porter encourages his daughter to stay with the man she loves, and Jane jumps overboard to return to shore; Porter shortly follows her, telling the non-money-grubbing captain to tell the British that the crew never found them. The two are accepted into the gorilla troop where, as the song says, they are all finally "Two Worlds, One Family" And All Thanks To The Courageous Help of Dave Felis, And Bucky O'Hare The Heroes of The Earth And The Aniverse.

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