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Jonathan Archer is Captain of the NX class starship, Enterprise.
Following humanity's invention and tests of the Warp Drive technology(which Jonathan and his father, Henry, played no small part), and with careful monitoring by the Vulcan race, the Enterprise is commissioned on a peaceful mission of science, exploration and diplomacy.
In the game, Star Trek: Legacy, Jonathan Archer is the first of the five Captains to encounter the vulcan Turell; the game's antagonist. Archer rescues Turell from a Romulan attack. Turell then convinces Archer to escort her to a research station, where she fears her colleagues are in danger of Romulan attack. Under this pretense, Arhcer is tricked into protecting Turell while she collects her research and escapes, neglecting to save the people on the station as it explodes.
The game then continues on through the other Captains of the Star Trek franchise, where it is learned that Turell's master-plan is to create a Vulcan/Borg uber-species. In her megalomania, Turell believes that this species will be purest in logic and the purging of emotion.