Plot continue

Despite Grace's argument that destroying Hometree could affect the bio-botanical neural network to which Pandoran organisms are connected, Selfridge gives Jake and Grace one hour to convince the Na'vi to evacuate. When Jake reveals his original mission, Neytiri accuses him of betrayal, and Jake and Grace's avatars are tied up. Quaritch's forces destroy Hometree, killing Neytiri's father, as well as many others. Mo'at frees Jake and Grace, but they are unplugged and imprisoned. Trudy, a pilot disgusted with Quaritch's brutal methods, breaks them out and flies them to an avatar link outpost. During the escape, Quaritch shoots and seriously wounds Grace.

The Na'vi fight back but suffer heavy casualties; Tsu'tey and Trudy are killed. Just when all seems lost, Pandoran wildlife suddenly join the attack and overwhelm the humans, which Neytiri interprets as Eywa answering Jake's prayer. Jake destroys a shuttle converted into a makeshift bomber before it can reach the Tree of Souls. Just before his own ship crashes, Quaritch dons an AMP suit and breaches the avatar link unit containing Jake's human body, exposing Jake to Pandora's poisonous atmosphere, before Neytiri kills him. She gets to Jake in time to save him. They reaffirm their love as she sees his human body for the first time.

With the exception of Jake, Norm, Max, and several other scientists, all humans are expelled from Pandora (including Selfridge). Jake is seen wearing the insignia of the Omaticaya leader. The clan performs the ritual dedicated to Eywa that permanently transfers Jake from his human body into his avatar.

Reference: http://www.avatarthemovie.com.au/