More than a decade after the Na'Vi repelled the human invasion of Pandora, Jake Sully (Sam Worthington) (a former human who fell in love with Neytiri and befriended the Na'Vi after becoming a member of the Avatar Program, eventually taking their side in their conflict with humans and leading them to victory. He left his human body to permanently become one of the Na'Vi) lives as chief of the Omaticaya clan and raises a family with Neytiri (Zoe Saldaña), which includes his sons, Neteyam (James Flatters) and Lo'Ak (Britain Dalton); his biological daughter, Tuk (Trinity Jo-Li Bliss); his adopted daughter; Kiri (Sigourney Weaver) (born from Grace Augustine's inert Na'Vi avatar); and a human boy named Miles Socorro "Spider" (Jack Champion), the son of Colonel Miles Quaritch (Stephen Lang) (Colonel Miles Quaritch, a human who led the security forces of the RDA, the human organization colonizing Pandora, in their conflict with the Na'Vi) who was born on Pandora and was unable to be transported to Earth in Cryostasis due to his young age.the Na'Vi sent all the humans back home, but kept the scientists like Norm and Max, to help continue their study of the Na'Vi ecology and biology. To the Na'Vi's dismay, humans return to Pandora to prepare it for colonization, as Earth is dying. They erect a new main operating base named "Bridgehead City". Among the new arrivals are "Recombinants", Na'Vi avatars with the memories of deceased RDA marines, with Quaritch's Recombinant as their leader. General Frances Ardmore (Edie Falco) is the commander in charge of the planet.Jake initiates a guerrilla campaign against the RDA supply lines by attacking a Maglev train carrying weapons. Quaritch and his Recombinants conduct a counterinsurgency mission against Jake (they are dropped close to the magnetic mountains in the hope that the Na'Vi DNA will not trigger the immune response from the local ecosystem), capturing his children (The children come across Miles's team looking for footage of their last encounter with Jake and Neytiri, when they are cut off and captured by Miles. Spider learns that Miles is his father and that he was killed by Neytiri). Jake and Neytiri arrive and free most of them, but Spider is taken by Quaritch, who recognizes him as his son. He decides to spend time with him in order to draw Spider on his side, and in turn, Spider teaches Quaritch about Na'Vi culture and language.Aware of the danger Spider's knowledge (he knew their entire base and tactics of operations) of his whereabouts poses to their safety, Jake and his family exile themselves from the Omaticaya and retreat to the Metkayina reef people clan at Pandora's eastern seaboard, where they are given shelter, even though some tribesmen consider them to have "demon blood" for their genetic human heritage. The family learns the ways of the reef people, Kiri develops a spiritual bond with the sea and its creatures (she gets the ability to summon and command them), and Lo'Ak befriends Tsireya (Bailey Bass) (a graceful and strong free diver of the Metkayina), the daughter of clan chief Tonowari (Cliff Curtis) and his wife Ronal (Kate Winslet) (a free diver of the Metkayina and Tonowari's wife, who is pregnant). Jake tells Tonowari that he has left the war behind him and only seeks safety of his family. He is allowed to stay, and Jake is very keen to ensure that his family respect the ways of the MetkayinaLo'Ak gets into a fight with Tsireya's brother Aonung (Filip Geljo). When he returns to apologize at Jake's insistence, Aonung and his friends entice him to a trip into the territory of a dangerous sea predator and leave him stranded on purpose and far away from their village. Lo'Ak is attacked by the predator and is about to be killed, when it is saved by and befriends Payakan, a Tulkun, an intelligent and pacifistic cetacean species whom the Metkayina consider their spiritual family. Payakan is a loner and sees Lo'Ak also as a loner and hence saves him. Upon his return, Lo'Ak takes the blame on himself, winning Aonung's friendship, but is told that Payakan is an outcast among his species.On a trip to the Metkayina's Tree of Souls, Kiri links with it to meet her mother, but suffers a violent seizure. She is healed by Ronal, but when Jake calls Norm Spellman (Joel David Moore) and Max Patel (Dileep Rao) for help, Quaritch is able to track them to the archipelago where the reef people live. Bringing Spider with him, he commandeers a whaling vessel (led by Captain Mick Scoresby (Brendan Cowell), the head of a private sector marine hunting vessel on the planet of Pandora & Dr. Ian Garvin (Jemaine Clement), a marine biologist) which is hunting Tulkuns to harvest their brain enzymes for creating anti-aging remedies named Amrita. Quaritch begins to brutally question the indigenous tribes about Jake's location; failing that, he orders the whaling crew to wantonly kill the Tulkuns in order to draw Jake out. Lo'Ak mentally links with Payakan and learns that the Tulkun was cast out because he went against the ways of his species and attacked the whalers who killed his mother. In the attack, many Tulkun were killed and Payakan was blamed for using violence and violating the ways of their species.When the Metkayina learn of the Tulkun killings, Lo'Ak takes off to warn Payakan, followed by his siblings, Tsireya, Aonung and Rotxo (Duane Evans, Jr.). They find Payakan being chased by the whalers, and Lo'Ak, Tsireya, and Tuk are captured by Quaritch. With their children in danger, Jake, Neytiri, and the Metkayina set out to confront the humans. Quaritch forces Jake to surrender, but seeing his soul brother imperiled, Payakan attacks the whalers, triggering a fight that kills most of the crew and critically damages the vessel, causing it to sink. Neteyam rescues Lo'Ak, Tsireya and Spider, but is fatally shot and killed. Jake faces Quaritch, who uses Kiri as a hostage. When Neytiri does the same with Spider, Quaritch at first denies his relationship with him but desists when Neytiri cuts Spider across the chest. A fight ensues between Jake and Miles as the vessel continues to sink.Jake, Quaritch, Neytiri, and Tuk end up trapped inside the sinking vessel. Jake strangles Quaritch into unconsciousness and is rescued by Lo'Ak and Payakan, and Kiri summons sea creatures to help her save Neytiri and Tuk. Spider finds and rescues Quaritch, but renounces him for his cruelty and rejoins Jake's family. After Neteyam's funeral, Jake informs Tonowari and Ronal of his decision to leave the Metkayina. Tonowari, however, respectfully identifies him as part of the clan and welcomes his family to stay. Jake and his family accept and forge a new life at sea, with Jake vowing to keep fighting the human invaders.