The RDA establishes "Bridgehead City" to prepare Pandora for full human settlement because Earth is dying. Recombinant Colonel Quaritch kidnaps Spider, identifying him as his biological son. While Spider refuses to betray the Na'vi language and secrets outright, Quaritch uses his familiarity with Jake to hunt the Sully family across the archipelago.
Quaritch commandeers the SeaDragon, an industrial whaling vessel captained by Mick Scoresby, and begins butchering sacred Tulkuns to draw Jake out. Payakan—an outcast Tulkun who previously led a failed assault on whalers that cost the lives of other Tulkun—defies the species' strict pacifist doctrine and attacks the RDA vessel, turning the tide of the battle.
During the chaotic confrontation, Neteyam (Jake and Neytiri’s eldest son) is fatally shot while rescuing Spider and his siblings. The SeaDragon is wrecked and begins to sink. Jake engages Quaritch in a brutal hand-to-hand fight inside the flooded vessel, rendering him unconscious underwater. Lo'ak rescues Jake using the Way of Water breathing techniques, while Kiri commands bioluminescent sea creatures to guide Neytiri and Tuk out of the flooded wreckage.
Spider discovers the unconscious Quaritch underwater and pulls him to safety, but refuses to join him, choosing to return to Jake and Neytiri as an adopted son. The Sullys hold a traditional funeral for Neteyam in the reef, laying him to rest within the roots of the Metkayina Spirit Tree. Jake accepts that they can no longer run from the RDA and vows to make their final stand on the oceans of Pandora.