Opening scene: a camera sweeps high across the treeline of a lush, green world.
Intercut is a sequence of images of Jake Sully (Sam Worthington) waking up in a VA hospital, where he is one of a seemingly endless number of wounded war veterans. Jake awakens inside a pod-like apparatus, where he's comforted by hospital staff. Then, through voiceover and dialogue with both hospital and military officials, we learn that Jake has a recently deceased twin brother -- Tom, a scientist -- who was to be part of a highest-level program overseen by corporate and military strategists. Because Jake and his brother are genetic matches, he's presented with a unique opportunity: take over his brother's contract with with corporate-military entity and travel light years away to an outpost on the previously glimpsed world, Pandora.
Acknowledging the notions of "being free" and having a "fresh start", Jake agrees to the deal as his brother's body is cremated.
Now aboard a human transporter spacecraft, Jake is one of many soldiers and personnel about to touch down on Pandora, actually a moon of the planet of Polyphemus, some 4.3 light years from Earth. We catch views of the base and its construction as Jake ponders his new role. Then, as the other passengers disembark and take their first steps onto the base, we see Jake make his first pushes into this world, for Jake is in a wheelchair. Jake acknowledges through voiceover that he lost the use of his legs during one of his tours of duty on Earth, and while a spine can be fixed, that "takes money," and that is tough to come by in the present economy. To add insult to the situation, Jake is referred to as "Meals on Wheels" by a few of his fellow travelers who are about to begin their careers as for-hire workers on Pandora.
Cut to a military briefing room, where Colonel Miles Quaritch (Stephen Lang) is addressing the assembled soldiers, including Jake. Referencing the fact that they're "not in Kansas anymore," Col. Quaritch educates the soldiers on Pandora's indigenous population, the Na'vi. Quaritch lets it be known that the Na'vi want to kill and, while it's his job to keep soldiers alive, he will not succeed in this task -- "not with all of you," he declares.
Jake is now in a science lab where he meets biologist Norm Spellman (Joel Moore) and Dr. Max Patel (Dileep Rao), two members of the Avatar Program. As Jake gets his first look at his own Avatar, we learn about the program itself.
Humans are unable to breathe Pandora's air, but the Avatar Program enables people to link with their own Avatar, a genetically-bred human-Navi hybrid. Through his Avatar body, Jake will be able to walk again. While Jake says his Avatar "looks like Tom," Norm replies that the being "looks like you".
We learn more about the program as Jake records his experiences onto his videolog (the first of many). During this, Dr. Grace Augustine (Sigourney Weaver), the program's science lead, awakens. We learn that she likes "plants better than people," and after speaking in Na'vi with Norm, she informs the assembled group of people that she needs Tom, a Phd.D who trained 3 years for the Pandora mission, and that she has no use for Jake.
Grace is next seen in the base's control room with Parker Selfridge (Giovanni Ribisi), representative for the Resources Development Administration, an organization that oversees all military and other personnel on the colony. Grace tells Parker she needs a researcher and not a "jarhead dropout" when told that Jake will serve as a security escort on her team while they're on the planet's surface. Grace is doubtful that Jake possesses the skills to meet one of her objectives: to bond with the Na'vi and discern the factors for the breakdown in Na'vi/human relations. Parker has a different goal. After discussing Pandora's much-desired natural resource, the mineral Unobtanium, which can save Earth from its present energy crisis. Parker wants Grace simply to "use what you got and get me some results."
Back in the lab, Jake and Norm are linked to their Avatars for the first time. It's noted that Jake's brain is "gorgeous". Jake, in his Avatar, wakes up in a different room with other Avatars and staff. Within a few moments, Jake is making his handlers nervous because he is moving too quickly and trying to walk. His long tail is knocking over instruments. A staff member informs him that his behavior is dangerous, to which Jake replies, "This is great".
Jake busts out of the recovery room and into the daylight. He finds himself in a recreation area where other Avatars are playing sports and staff, in their protective gear, are performing various duties. Norm is in pursuit of Jake. When Avatar Jake dips his toes into the dirt, we're shown how the feeling registers on the face of human Jake.
In the garden area, Jake meets Grace's Avatar, who, with a slightly more cheery demeanor, accompanies Jake to the barracks where he is eventually encouraged to rest. The link is broken, and human Jake awakens.
Jake next meets Trudy Chacon (Michelle Rodriguez), a retired Marine pilot with whom he'll spent several weeks getting used to his Avatar and exploring Pandora. Jake will also serve as the door gun on her crew.
Jake reunites with Col. Quaritch, who is lifting weights. The Col. Tells Jake about some of his tours, including one in Venezuela, and other aspects of his military history. The Col. re-warns Jake about the dangerous awaiting him on Pandora. His also exerts his belief that the Avatar Program is a joke and that it actually represents an opportunity for a unique reconnaissance mission: Jake can amass knowledge of the "hostiles" and "savages" as a covert military operative. At the end of this scene, the Col. climbs into an AMP Suit -- a bipedal exoskeleton used for missions on Pandora -- and informs Jake that he will help get his real legs back.
Relinked with his Avatar, Jake is flying over Pandora's surface with Trudy, Grace, Norm, and others. The team lands in a forest setting, where Grace and Norm begin to take different samples. Jake is distracted by his surroundings and making Grace nervous. He wanders into a field of Helicoradian flowers, which are quite tall and shrink at Jake's touch. Trouble arrives when a Titanotheres -- a dinosaur-like creature -- confronts Jake. Grace orders him to stand his ground and not shoot, or else the animal will charge. Jake successfully holds his ground, but only because a larger creature, a Thanator, has approached him from behind. Grace tells Jake to run -- definitely run -- and he's pursued by the Thanator in a chase that separates Jake from his crew. Initially, Jake eludes the beast; even when he's lost his gun and then downed by the animal, he releases his pack to escape. Ultimately, the chase leads to waterfalls, where Jake jumps to his safety, leaving the Thanator alone above him.
Now on dry ground, Jake is fashioning a spear and then a torch as we notice he's been watched above, this time from a different being ... a Na'vi? It has to be. The being draws an arrow to a bow and is about to shoot, only to be surprised as seeds (we'll come to know them as the "seeds of Eyra") land on the bow and arrow. The being retreats.
Meanwhile, as Jake's crew searches for him, Trudy says they'll have to return to base since night ops are not allowed. It's acknowledged that Jake likely will not survive until the morning.
As Jake fashions a torch, he's surrounded by a pack of Viperwolfs, who encircle Jake with their teeth bared, jaws gnashing. As their battle begins, the being who was observing Jake joins him in the battle, where she kills many of the animals and causes the rest to flee. Now alone, Jake follows his rescuer to an illuminated pond, where prayers are said for the animals that were killed. Spent arrows are then collected. Jake says thanks for killing those "things" which earns an agitated response from his rescuer, who hits Jake with the arrows and declares that the animals did not need to die. Jake is then told the incident is his fault because he is "like a baby" yet he's also told the reason he was saved was due to his strong heart and lack of fear.
Though no introduction has been made yet, Jake follows his rescuer up into a tree, though he's warned that he, like the other "sky people", should not be on Pandora. Just then, the seeds of Eyra reappear and we learn they are seeds of a sacred tree -- "very pure spirits" -- and Jake is covered by them. "Come," he is told.
In this next scene, we learn the name of Jake's rescuer: Neytiri (Zoe Saldana), who is young Na'vi female. Netyiri presents Jake to her people, the Omaticaya, though he is surrounded by Omaticayan warriors and felled by them. Leading this group of men is Tsu'Tey (Laz Alonso), Neytiri's brother and next in line to the throne. Neytiri lets them know that "there has been a sign" and that he should be brought to "tashik" (father, approximate spelling) and "eyra" (mother).
Jake is presented to Neytiri's parents, Eytukan (Wes Studi) and Mo'at (CCH Pounder), who are the king and queen of the tribe, respectively. Jake tells the elders that he is a warrior -- a "dreamwalker" -- and his intention is to learn from the,. Mo'at tastes Jake's blood from a wound on his forehead and decrees it is the will of Eyra for him to live with the Omaticayan, and for Neytiri, however reluctantly, to be his teacher in their ways and customs. After a ritual gathering, Jake is brought to his bed, a leaf high up in the "Hometree" that encircles him like a cocoon. As he falls asleep, human Jake is revived.
At morning chow, all the scientists, including Grace, are focused on every one of Jake's words. Even the military and corporate reps have warmed to him. He lets them know the Hometree rests on Pandora's biggest deposit of Unobtanium. He's informed that he has three months to achieve his objective.
The next series of scenes revolve around Avatar Jake's training with Neytiri and human Jake's reported findings. He bonds with his Direhorse, arguably the most important animal to the Na'vi since Jake must learn to must mount the animal and connect his neural queue to its antennae. Human Jake continues to report on the Hometree's infrastructure and other Na'vi details.
Jake takes his first trip to the Hallelujah Mountains -- a system of remote, floating islands that are sacred to the Na'vi and are also rich in Unobtanium. It's here that Grace's camp is to be set up, away from the RDA officials and military officers alike.
In his next videolog, Jake discusses his language lessons and says his time with the Na'vi is like "field-stripping a weapon". This is intercut with scenes of his continued training with Neytiri, who teaches him about the Na'vi-forest connection. She tells Jake that all energy is borrowed and one day we have to give it back. Jake seems to comprehend this, and as he says a prayer for an animal he successfully hunted, Neytiri says that he is "ready".
We discover that Jake is ready for a Na'vi rite of passage: to connect with a Mountain Banshee, a flying creature, in the same manner he bonded with the Direhorse. Several factors (the height, the ferociousness of the untamed banshees) make this a dangerous lesson, but Jake's lack of fear and successful bond with his Banshee impress the Na'vi warriors present, including Tsu'Tey. Jake, Neytiri, and the others ride together to the Tree of Souls, the most sacred place to the Na'vi.
Human Jake is revived, and Grace calls him a "lucky swine".
Jake next is on an aerial hunting mission. Pursued by a creature known to the Na'vi as Toruk, which is larger than his Banshee. Neytiri says one name the beast has earned is "last shadow" and that her grandfather once rode on of the animals to unite the 5 Na'vi tribes.
When Jake comes back to, it's clear he's been changed by this latest experience, for he says, "out there is the real world ... in here is the dream". He's then confronted by the Colonel to say he's to take a shuttle to get his legs back, but Jake asks to delay the trip, since this evening there is to be a ceremony where he will become a true Na'vi man. The Col. acquiesces when Jake says this will be the perfect opportunity to negotiate the relocation of the Omaticaya so RDA can claim the Unobtanium.
Cut to the ceremony, where Jake learns the Na'vi believe that every person can be born twice. Neytiri leads Jake to a place of prayer, the "tree of voices" where they bond with the tree. Neytiri tells Jake he can made a bow from the tree ... and that he can choose a woman.
Jake says, "she must also choose me".
Neytiri indicates, "she already has".
In the morning, Neytiri awakens to falling tress, then the presence of bulldozers. She cannot wake Jake (back on the base, Jake is having breakfast and is clearly in a clear rush to return to Neytiri). Soldiers are advancing, the forest is falling around Neytiri, who is dragging and carrying Jake to safety. When he finally revives, Jake climbs onto one of the flying craft and tries to stop it, eventually blinding their camera system and initiating some gunfire. Other Na'vi warriors arrive, while the assembled military personnel recognize Jake in his Avatar form as the person who tried to stop their mission.
At Hometree, the Na'vi want war. Grace and Jake say no. There's an intense debate. Tsu'Tey tries to kill Jake. Jake declares he is a Na'vi and deserves the right to speak. Then, suddenly, both Grace and Jake's Avatars are downed.
Grace and Jake face off with RDA and military brass. It's revealed that Pandora has a "network of trees" and that the Omaticaya will never leave Hometree. Parker and the Col. discuss options. Gas out the Na'vi ... turn gunships on Hometree ... Jake lobbies to return to the Omaticaya and negotiate, and he's granted one hour to achieve the objective.
Jake and Grace are not welcomed back. Neytiri rejects Jake. Both are bound and left behind by the Omaticaya, who are preparing to fight against the humans.
Gas canisters are launched into Hometree and the surrounding area. Rockets are fired. The military is advancing on the ground and in the air. As the battle escalates, most of the weaponry is focused on Hometree, which is downed by a series of explosions and heavy artillery. Many Omaticaya are killed. Moat frees Jake and Grace and asks them to save the tribe. We watch a dying Eytukan tell Neytiri to take his bow and protect their people. Jake then arrives and is rejected again by Neytiri when he tries to console her.
The destruction seems endless, and, suddenly, Jake and Grace return to their human bodies and promptly placed under arrest for treason. Norm is also arrested for trying to prevent soldiers from disabling their Avatar forms.
Some time has passed, and the Na'vi exodus continues.
Trudy arrives at the cell which holds Jake, Grace, and Norm. She dupes their guard by saying she wants nothing to do with them, only to knock out the guard an instant later. In the attempt to flee the base in Trudy's ship, Dr. Patel remains behind while Grace is shot by the Colonel, who braves Pandora's atmosphere without protection, hell bent on recapturing Jake and the others. The team flies to the Tree of Souls, where the Omaticaya have relocated.
The hopeful reunion with the Omaticaya is not to be, initially. Jake is outcast, an alien. He does, however, convince Mo'at to try and help a dying Grace. Mo'at agrees and begins the preparations, mostly which involve getting Grace in place at the Tree of Souls.
Ever more determined to make amends with the Omaticaya, Jake arrives from the sky on the back of a Toruk in front of the Tree of Souls. The stunned Omaticaya feel Jake's dedication to them; in an exchange with Neytiri, she says "I see you". Tsu'Tey, who is now king, and Jake also make amends.
Back to Grace's ritual. The attempt is to try and have Grace's consciousness permanently transferred to her Avatar self. We see both human Grace and her Avatar. Mo'at lets it be known that Grace must pass through the eye of Eyra, and that the great mother might choose to let her pass through to her Avatar self, or she might opt to have Grace remain with her. The ritual is not successful, though before she dies, Grace tells Jake that she has seen Eyra. Jake is next seen addressing his chosen people. He says it's time to bring war to the sky people, and to do so, the other Na'vi clans must be brought together to fight as one.
The military, who are about to launch their attack, are focusing most of their efforts on turning a single craft into a massive bomb. Their target is, of course, now the Tree of Souls, and the attack is planned for 0600 the next day.
Jake is busy rallying the Omaticaya. At the Tree of Souls, he looks into Grace's memories, realizing that humankind killed their mother (Earth), the entity that protects the balance of life.
The story quickly jumps to the day of the final battle. The military forces are close and the bombship is hovering toward the Tree of Souls. Because of Pandora's magnetic currents, however, human-made instruments are failing. The united Na'vi force begins to arrive from the sky and on the ground. On his Toruk, Jake, Tsu'Tey, and other warriors engage in battle with the military craft, mainly Scorpion and Dragon assault ships. Casualties are mounting on both sides.
A flurry of main-character action: Jakes locks onto Colonel Quaritch; Trudy arrives and opens fire; Neytiri is separated from her Banshee; Norm's Avatar is mortally wounded and he jumps back to his human form; Tsu'Tey takes on the bombship and is killed in the attempt; Trudy's ship is blown up and she is killed in the process.
On the ground, Neytiri watches this action transpire. Jake attempts to contact Tsu-Tey and is unsuccessful, as is his attempt to reach Neytiri. The bombship closes in on the Tree of Souls.
A reunited Jake and Neytiri opt to stand their ground against the humans but to no longer display aggression. Suddenly, through what's left of the surrounding forest, a battalion of Pandora's animal races arrive. Neytiri tells Jake, who called out to Eyra for help earlier, has been heard as the various animals engage in combat with the humans.
Jake and his Toruk take to the sky to confront the bombship as the military's ground forces begin to scatter. Jake grenades the bombship and it catches fire.
Colonel Quaritch mans an AMP Suit in preparation for battle on the ground. He makes his way to the temporary camp set up by Grace and the others when they escaped from military incarceration. Human Jake, of course, is inside the camp and linked to his Avatar self. Quaritch is set on killing Jake, and Neytiri arrives with seconds to spare and saves Jake, though her Thanator is killed and she is trapped underneath it.
Avatar Jake arrives and engages Colonel Quaritch in a fight, and the Col. is quickly injured, but Jake is caught in the grip of the AMP Suit. Meanwhile, Neytiri has almost freed herself. Out of his AMP Suit, the Colonel dons a breathing device and insults Jake, asking him how it feels to have betrayed his race. The Col. races to the camp and is surprised when he doesn't find Jake in the first pod. Human Jake is starting to unlink with his Avatar self.
With human Jake in the Col.'s clutches, Neytiri draws an arrow and downs her enemy. A second arrow brings him to the ground. However, much damage has been done to the camp, which is leaking oxygen. Human Jake is awake but having difficulty both breathing and trying to get a mask on. Fully in danger, Neytiri arrives to help Jake with his mask. Neytiri, cradling Jake, says, "I see you".
Cut to the former military base, which is now under Na'vi control. Most of the remaining humans are being rounded up to be shipped back to Earth; however, some of the more harmonious people are invited to stay on Pandora. Norm is one of the humans who will remain.
Jake signs off in his final videolog, where we learn that he has chosen to transfer his consciousness to his Avatar self. In a ceremony similar to Grace's, Jake passes through the eye of Eyra ... and wakes up in his Avatar self with Neytiri watching over him.
