The film starts with Lo’ak (Britain Dalton) reliving a memory with his late brother Neteyam (Jamie Flatters) as they ride their Ikrans across the sky. Lo’ak continues to blame himself for Neteyam’s death due to his actions in battle. Meanwhile, Kiri (Sigourney Weaver) and Spider (Jack Champion) appear to be forming more than a friendly connection.
Neytiri (Zoe Saldana) continues to grieve her son and immerses herself in old Na’vi traditions to cope, while Jake (Sam Worthington) leads his kids to recover guns from sunken ships. The Metkayina are none too pleased at the thought of utilizing guns in the fight against the RDA, putting Jake in conflict with Tonowari (Cliff Curtis) and Ronal (Kate Winslet). Tonowari suggests that Jake take up his position as Toruk Makto again, but Jake thinks riding the Toruk will make him someone he doesn’t want to be.
The RDA continue to scour wreckages for whatever they can recover. Scoresby (Brendan Cowell) survived his attack and now uses a prosthetic arm. Ardmore (Edie Falco) has lost trust in Quaritch (Stephen Lang), who is still driven by his desire for revenge against Jake. Meanwhile, Ian (Jemaine Clement) starts to question his loyalty to the RDA.
Lo’ak, Kiri, and Spider join Tsireya (Bailey Bass), Aonung (Filip Gejlo), and Rotxo (Duane Evans Jr) in swimming along Payakan, who is still considered an outcast among the other Tulkun for using violence. Later at night, the family wakes up in a panic as Spider’s oxygen mask starts to run out, but he is given a replacement in time.
The Metkayina are visited by the Wind Trader tribe. Jake breaks the news to Lo’ak, Kiri, Tuk (Trinity Bliss), and Spider that he and Neytiri have decided that Spider ought to be taken with the Wind Traders to live somewhere he might be able to breathe properly. The kids protest, with Spider tearfully asking Jake to reconsider, but Neytiri outright tells Spider that he will never be part of their family. Jake arranges with the Wind Trader leader Peylak (David Thewlis) to allow the family to join them in escorting Spider to his new home, on the condition that Neytiri protect them from the skies.
The Sullys ride with the Wind Traders in their airships, which come under attack by the Mangkwan tribe, a ruthless group of fire-based Na’vi lead by their vicious leader Varang (Oona Chaplin). A sky battle ensues, with the Mangkwan shooting several warriors out of the sky, but the Sullys fight back with their own firepower. Kiri gets Lo’ak, Spider and Tuk out on an Ikran, while Neytiri is knocked into the forest by Varang. The kids crash-land in the forest as well. They witness Varang and other Mangkwan connecting their kurutails to other Na’vi to overpower them and then cut their kurus off. The kids are chased, but they manage to kill a few Mangkwan before escaping.
As the kids continue to run, Spider’s oxygen mask starts to run out until it is completely gone. Desperate, Kiri uses her kuru to connect to the earth, which then covers Spider’s body in mycelia after she orders Lo’ak to put him there. After a while, Lo’ak pulls Kiri out, and it seems as though Spider is dead. However, he begins to move and breathe, and he no longer needs a mask to breathe Na’vi air. They are discovered by Varang and the Mangkwan, who also note Spider’s new development before they capture the children. When Kiri says that Spider breathing is the will of Eywa, Varang snarls that Eywa has no dominion in their territory.
Jake is caught by Quaritch and Wainfleet (Matt Gerald), but they form an uneasy alliance when they find the kids captured, and Quaritch realizes Spider is in danger. He reluctantly frees Jake, and they work together to fight the Mangkwan, but they are overpowered. Quaritch willingly shows Varang how guns work (or “make thunder”). Kiri connects herself to the earth again, causing the plant life to shoot toxic quills at the Mangkwan, giving everyone a chance to flee the villainous tribe.
Neytiri wakes up in a medical tent with Mo’at (CCH Pounder) and worries for the children. Meanwhile, Jake and Quaritch hold off on killing each other until the kids get home safe. Jake tries to convince Quaritch to see the world through new eyes now that he is a Na’vi, but he knows he is not going to “see” people the way the Na’vi do. Quaritch returns with Wainfleet to the RDA base to meet with Ardmore and Parker (Giovanni Ribisi), the latter who is still hoping to colonize Pandora and believes Spider’s newfound breathing capabilities can help with that. Norm (Joel David Moore) and Max (Dileep Rao) conduct tests on Spider’s anatomy. Norm shows Jake that Spider has grown his own kuru in the back of his head.
Kiri tries to connect to Eywa again, but she finds herself being shut out. When telling her family about it, Mo’at tells Jake and Neytiri to reveal the truth of Kiri’s parentage. She has no biological father and is instead a clone of Grace Augustine’s Avatar, not her daughter. Kiri is warned that if she tries to connect to Eywa again, she could kill herself. Jake privately talks to Neytiri, who suggests that they kill Spider or risk having the RDA figure out how to reverse engineer his breathing capabilities for their colonization efforts.
Scoresby and his goons continue to hunt the Tulkun with harpoons and other water vehicles. The Sullys return to the Metkayina, where Tonowari tells Jake that the Tulkun council are calling for a meeting regarding Payakan since he attacked a ship, while Ronal tends to Neytiri’s wounds. The Tulkun Matriarch orders Payakan to go into exile, which devastates Lo’ak. When he and Tsireya try to protest for Payakan, Jake intervenes and argues with his son, almost explicitly blaming him for Neteyam’s death for disobeying orders before Lo’ak runs away in tears. Jake talks to Neytiri about this, as she is still driven by her hatred for humans. Lo’ak comes close to committing suicide with a rifle until he is found by Kiri and Tsireya, who try to talk some sense back into him.
The teens are gathered in the ocean. Kiri starts to show Spider how to use his kuru to form a queue connection with the Pandoran wildlife, like the Skimwings underwater.
Quaritch and Wainfleet go looking for Spider by terrorizing other Na’vi. Quaritch then decides to go straight to the Mangkwan camp to speak to Varang. After having Wainfleet snipe one of the Mangkwan to prove he is not messing around, Varang brings Quaritch into her tent. She explains her people’s history, how the fire ravaged their homes and how they lost faith in Eywa when nothing helped them. The Mangkwan adapted to the fire, and Quaritch shows Varang how to use other weapons like a flamethrower. The two then begin a sexual relationship.
Tsireya tells Lo’ak that Payakan’s song was heard in nearby waters, which prompts him to leave home and look for him, but not without telling Neytiri first. He is joined by Tsireya, Aonung, and Rotxo to go search for the young Tulkun. Tonowari informs Jake that their children have gone.
Spider and Kiri are in the woods, where they share their first kiss. Moments later, Quaritch leads the Mangkwan to capture Spider, after Varang subdues him with her queue connection. The RDA and Mangkwan start heading toward the Metkayina village. When Quaritch and Varang emerge, Jake willingly surrenders himself to prevent them from harming the other Na’vi. Quaritch brings Jake and Spider back to base, and everyone greets Quaritch and Varang as heroes.
Lo’ak and the other teens are riding their Skimwings to find Payakan, but they are attacked by squid-like creatures. Lo’ak is cornered underwater and nearly drowns until the other Tulkun devour the squids, and Tsireya and the other boys pull Lo’ak out and resuscitate him. Later that night, Lo’ak reunites with Payakan, who tells him that he found the last surviving member of his family, another Tulkun named Ta’nok who was attacked and blinded by Scoresby’s harpoons. The bastard himself is planning to attack a school of Tulkun, which Ian openly protests.
At the RDA base, Quaritch tries to calm an angry Spider before going to taunt Jake, who is in a glass cage for everyone to see. Jake once again tries to get Quaritch to open his mind, but he refuses. Spider escapes his cell and disguises himself to blend in with the crowd, while Neytiri hunts her way to the base after killing some Mangkwan. She catches Varang sleeping and forces her to give up Jake’s location before Neytiri cuts off her kuru. A fight breaks out and Neytiri runs, setting off a panic after she blows up a tanker. Ian seizes the opportunity to use a giant bulldozer to break Jake’s cage and free him. Spider catches up to Jake and protects him, knowing the RDA will not shoot him since they need Spider alive. Jake and Spider join Neytiri as they fly to their escape.
When the three find a quiet place in the forest to land, Jake reconsiders Neytiri’s suggestion about killing Spider to get the RDA off their backs, which she has started to have second thoughts on herself. Jake brings Spider somewhere quiet, preparing to execute him even as Spider begs him not to. Jake ultimately cannot bring himself to do it and embraces the boy. Neytiri runs toward them and tells Spider that she finally “sees” him.
The Metkayina continue to refuse to engage in violence against the RDA, until Lo’ak brings Payakan and Ta’nok to them to show what the humans have done. Even as Payakan is still considered an outcast, Lo’ak and his friends, and their Tulkun all decide that they are outcasts as well. Jake then decides he must be Toruk Makto again and goes to a cave to get Toruk out so they may fly again in battle, as he warns the clans that a battle with the “Sky People” is inevitable.
The RDA prepare to go off into battle, with Ardmore trying to ground Quaritch for going against her orders, but he is determined to get Spider back. The battle begins as the Tulkun attack the whalers in retaliation. The Na’vi fight back against the humans and take out a good number of them before the Mangkwan swoop in to fight as well. Kiri dives underwater to reconnect with Eywa to try and help. When she is nearly overpowered, she is joined by Spider and Tuk connecting their queues to Eywa as well. Just when it looks like they finally see Eywa’s face, a blast goes off underwater, severing Kiri’s connection. Meanwhile, other Na’vi like Rotxo are fatally wounded, and Ronal takes a deadly hit as well. She gives birth to a daughter, Pril, and tells Neytiri to look after her before she dies.
Kiri is soon enveloped in a flash of light underwater, accompanied by other sea creatures. Now tapped into her connection with Eywa, Kiri commands the sea creatures to go after the humans. They destroy their ships, and Scoresby becomes a snack for one of them. Varang attempts to kill Neytiri, but Kiri catches up to her first and overpowers Varang by connecting to her queue and ordering her to flee, which she does. A magnetic flux opens up in the ocean, pulling the RDA’s head ship towards the vortex. Everyone abandons ship, but Ardmore goes up in flames with it. Quaritch makes another attempt on Jake after holding his kids hostage and ordering him to come with Spider. The boy willingly tries to give himself up, but Jake and Quaritch get pulled toward the flux and start fighting. Spider shoots Quaritch in the arm, but before he can deliver the killing strike, they are knocked over a ledge. Quaritch holds onto Spider, and Jake pulls them both up. When the rest of Jake’s family arrives, Quaritch realizes he is outnumbered and jumps off the edge and into the flames below.
Lo’ak narrates what happened afterwards. The other Na’vi begin to connect to Eywa as well. Payakan is finally accepted by his clan. Kiri brings Spider to the Tree of Souls, where he meets all the deceased Na’vi, along with Grace herself. The Na’vi now “see” Spider and all accept him as one of their own.[wide]

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