His father was a part of the early Starfleet team to help design the Enterprise, so it was only fitting that Jonathan took command. He grew up with a distrust of Vulcanss, since he perceived them as having held back Humanity's progress, particularly with regard to his father's Warp 5 engine.
He had the distinction of making Earth's official first contact with dozens of alien races, including the Andorians, the Axanar, the Romulans, the Tandarans, the Tellarites, the Tholians, and the Xindi.
Although initially optimistic, Archer became involved in his first mission as Captain of the Enterprise in the Temporal Cold War.
With the Xindi kamikaze attack on Earth, Archer became a changed man, determined to seek out and confront the perpetrators. This pushed him to commit desperate acts of questionable morality to ensure a future for Earth.
While on his mission to locate the Xindi, Archer was briefly transformed into a member of the extinct Osaarian species by a mutagenic virus. Shortly after, he was afflicted by subspace parasites and traveled back in time to 2004 Detroit.
[In early stages of writing, the character of Jonathan Archer was called Jeffery Archer.]