Summary
At the military base, Quaritch confronts Jake about the fact that he's let him down. "You say you want to keep your people alive? You start by listening to her," Jake tells Quaritch, referring to Grace. Grace tells him that the trees they chopped down were integral to the functioning of the forest and Pandora, on both a physical and a spiritual level. "It's more connections than the human brain...It's a network. It's a global network, and the Na'vi can access it. They can upload and download data. Memories," she tells the group. She explains that the Na'vi have access to this network and will never leave Hometree. Quaritch pulls up a video in which Jake is telling the camera that the Na'vi will never leave Hometree.
Rather than take this as a sign that their mission is doomed, Selfridge and Quaritch discuss their plans to use gas bombs to send the Na'vi packing. Jake begs them to let him go back to Pandora and try and convince the Na'vi to leave, and they tell him he has an hour.
When Jake and Grace return to Pandora, they are met with scorn and dismissiveness from the Na'vi. They try to explain that the Na'vi must leave, because Quaritch and his forces are coming, but the Na'vi are angry. Even Neytiri does not want to see Jake, and she screams in anger at him. As they prepare for a war with the humans, the Na'vi tie Grace and Jake up and leave them behind. When the military starts launching gas bombs at Hometree, the Na'vi try to fight back. The military resorts to more violent forces, and Hometree eventually falls, in a burst of flames.
Mo'at frees Jake and Grace and requests that they stop the violence. In the middle of the fighting, Trudy, who is flying a gunship, retreats, telling her commander that she "didn't sign up for this shit." When Neytiri's father, the king, Eytukan, is killed, he tells Neytiri that she is the new leader. Jake tries to comfort her, but she screams for him to leave and never come back. In the middle of the war, Jake and Grace are unlinked with their avatars and find themselves back in the lab. There they are arrested for treason, along with Norm. Meanwhile, the Na'vi meet at the Tree of Souls.
Jake, Grace, and Norm are held prisoner in a small cell. Trudy comes to save them by knocking the guard unconscious. She and Max release the group and they go to leave the base, but in the process, Quaritch shoots and wounds Grace. Undeterred, the group flies to the lab in the mountains, where they grab their pods and go elsewhere on Pandora, deep into the mountains, so Jake can link with his avatar once again without getting discovered by the military. On the ship, Jake takes care of Grace and suggests that the Na'vi will help her. "Why would they help us?" she asks him.
When he arrives back in his avatar in Pandora, Jake is not welcomed in, so he has to strategize something more impressive to win the Na'vi's trust. He decides that in order to regain their trust, he has to go and conquer the toruk and ride it. Riding on the back of his ikran, Jake determines that the best way to conquer the toruk is from above, so flies his ikran directly above, before jumping atop the toruk.
The Na'vi gather and sing at the Tree of Souls, when suddenly Jake flies overhead on the toruk. When he lands, the Na'vi scatter, screaming. Neytiri and the others look on, startled, and bow to him as he walks among them. He approaches Neytiri and she says, "I See you." "I See you," he responds, and they embrace.
He approaches Tsu'tey and tells him that he needs his help to fight the humans. Tsu'tey agrees to fly with him, and then tells them that he needs their help to heal Grace. He carries Grace to the Tree of Souls and lays her down in some moss, where the Na'vi heal her with the roots of the tree. Mo'at leads the Na'vi in a ritual to revive Grace. "I am with her, she is real," Grace says, and then dies. "She is with Eywa now," Mo'at says, and Jake weeps. Standing, he addresses the Na'vi, with Tsy'tey acting as a translator. He motivates the group, suggesting that they must rise and fight Quaritch and the others.
Analysis
The conflict between science and the military, between understanding and force, comes to a head when Quaritch takes Jake and Grace from their lab and questions them at the military base. Grace insists that the trees of Pandora are a network of synapses like the human brain that connects data and memories, but Quaritch and Selfridge remain skeptical. They do not want to hear about the biological makeup of the planet, they simply want to know how to extract what they came to get. In this conflict, we see a heated conflict between profit-chasing and information accumulation, between life-affirming research and life-destroying acquisition.
Grace explains to the military personnel that the trees that they are destroying on the planet are connected to one another and serve as a kind of biological simulation of the human brain. Root systems connect to one another like synapses in the brain, storing information and data in a complex and unusual system that is worthy of their protection. This finding has not only biological implications, but spiritual ones as well, in that the trees on Pandora represent a kind of cosmological system, one that connects various spheres of information from the past and the present in a complex system of data.
The split between the military and the scientists becomes even more intense when Quaritch has Grace, Norm, and Jake arrested and throws them in a cell. The military proves to be more powerful than the forces of science, strongarming the scientists into bending to its will, which makes the conflict more ruthless and intense than it has previously been. The scientists must become scrappy and resourceful, using their own force to battle with the military thugs who threaten the wellbeing of Pandora.
When he links up with his avatar once again, Jake becomes determined to win back the trust of the Na'vi by showing that not only is he one of them, but that he is their salvation against the violence of the military forces. He resolves to conquer the mythical toruk, and demonstrates that he is a true Na'vi by riding it. In doing this, he integrates himself into the ways of the Na'vi and proves that he is one of them, that he is literally the next in line to ride the toruk, a gesture that once united all the tribes of the Na'vi.
Jake's plan works, and he is able to integrate once again with the Na'vi people. He delivers a rousing speech to get the tribe on his side, and motivates them to fight for what is theirs against Quaritch and the troops. After all the injustices he has faced working under the military, and after seeing the integrity of the Na'vi people, Jake chooses his side once and for all, no longer acting as a double agent. Solidifying his desire for vengeance against Quaritch is the death of Grace, a victim of Quaritch's wrath.
