Jake was part of the Avatar Program, in which humans remotely control Human/Na'vi hybrids to safely navigate the planet. Jake was originally assigned to gather intel that would help Colonel Quaritch discover the Na'vi weaknesses so he could force them to leave Hometree or destroy it if necessary.

This being done so due to the earth beneath Hometree having a significant deposit of Unobtanium; the entire reason for RDA's interest in Pandora. Jake learns the ways of the Na'vi hunters from Neytiri and is eventually accepted into the Omaticaya clan. Soon after he and Neytiri fall in love.

Shortly after this the RDA stages it's attack on Hometree, for which Jake seeks revenge. When everything seems lost to the Na'vi, Jake is able to attain Tsahaylu with a Great Leonopteryx, becoming the sixth Toruk Makto.

He plays a key role in the final war, as he leads the Na'vi against the RDA offensive. The Na'vi then perform a ceremony in which they ask Eywa to place Jake's mind into his Avatar body permanently.