In 2154, humans have exhausted Earth’s natural resources, leading to lack of resources. The Resources Development Administration (RDA ) mines for a valuable mineral — Unobtanium on Pandora, a densely forest habitable moon. Pandora’s atmosphere is harmful to humans, is lived by Na’vi, a species of 10-foot tall, blue skin, big eyes and have high intelligence living things that live with nature and worship a mother goddess named Eywa. To explore Pandora, scientists use Na’vi-human hybrids called “avatars”.
Jake Sully, a retired Marine, replaces his identical twin brother as an operator . Dr. Grace Augustine, head of the Avatar Program, considers Sully is not a good choice but accepts him as a bodyguard. While protecting the avatars of Grace and fellow scientist Dr. Norm Spellman as they collect biological data, Jake’s avatar is attacked by a Thanator and flees into the forest, where he is rescued by a female Na’vi, Neytiri. Witnessing an auspicious sign, she takes him to her clan. Neytiri’s mother Mo’at, the clan’s spiritual leader, orders her daughter to teach Jake their cultures.
Colonel Miles Quaritch, the head of RDA, promises Jake will treat his legs if he collects information of the Na’vi and their gathering place, Hometree. The undergrounds of Hometree are rich of Unobtanium. When Grace knows of this, she transfers herself, Jake, and Norm to an outpost. It takes three months to let Jake grow into sympathizing with the natives. After Jake is blended into the clan, he and Neytiri choose each other as mates, and soon afterward, Jake shows his royalty when he tries to disable a bulldozer to destroy the sacred Na’vi site. Quaritch shows a video recording of Jake’s attack the bulldozer and Jake also admits that the Na’vi will never abandon Hometree ,then Administrator Parker Selfridge orders to destroy Hometree.
Despite Grace’s argument that destroying Hometree will damage the biological neural network native of Pandora, Selfridge gives Jake and Grace an hour to convince the Na’vi to evacuate before the attack. While trying to warn the Na’vi, Jake admits to being a spy and the Na’vi take him and Grace captive. Seeing this, Quaritch’s men destroy Hometree, killing Neytiri’s father (clan chief) and many others. Mo’at frees Jake and Grace, but they are separated from their avatars and imprisoned by Quaritch’s forces. Pilot Trudy Chacon, hated by Quaritch’s brutality, takes them to Grace’s outpost, but during the escape, Quaritch fires at them, Grace wounded.
To gain Na’vi’s trust, Jake connects with Toruk, a dragon like a predator feared and honored by the Na’vi. Jake finds the victim at the sacred Tree of Souls and pleases with Mo’at to save Grace. The clan tries to transfer Grace from human body into her avatar with the aid of the Tree of Souls, but failed. Supported by the new chief Tsu’tey, he acts as Jake’s translator, Jake tells them to gather all of the clans to battle with RDA. Noticing the gathering, Quaritch organizes a pre-emptive strike against the Tree of Souls, believing that its attacks will lower their morale. On the eve of battle, Jake prays to Eywa, to intercede on behalf of the Na’vi.
During the subsequent battle, the Na’vi suffers heavy casualties, including Tsu’tey and Trudy, but are rescued by Pandora’s wildlife unexpectedly join the battle, which Neytiri analyzes as Eywa answers to Jake’s prayer. Jake destroys a makeshift bomber before it can reach the Tree of Souls; Quaritch escapes from his damaged aircraft, wearing an AMP suit and breaks open the avatar link unit of Jake’s human body, exposing it to Pandora’s poisonous atmosphere. Quaritch prepares to slit the throat of Jake’s avatar, but Neytiri kills Quaritch and saves Jake.
Lastly, Jake and Norm select others to stay in Pandora, other humans are sent back to Earth. Jake was transferred to avatar in the end.