Editing Jonathan Archer (section)

===Season 3===
In Season 3, he was the military commander in the Expanse. Following the [[Xindi (Star Trek)|Xindi]] attack on [[Earth in fiction|Earth]] in 2153, Archer becomes a changed man.No longer a congenial captain, he is now driven and determined to seek out and confront the perpetrators. Archer commits desperate, controversial acts of questionable morality to ensure a future for Earth, including [[Anomaly (Star Trek: Enterprise)|torturing a prisoner]], [[Similitude (Star Trek: Enterprise)|cloning Tucker]] to harvest body parts to save the chief engineer and thus killing the clone, and [[Damage (Star Trek: Enterprise)|stealing a vital warp coil]] and leaving a ship of aliens stranded in space.<ref>{{cite web |date=April 23, 2004 |author1=Kate O'Hare |title='Star Trek: Enterprise's' Bakula Contemplates Ripples in Space |url=http://tv.zap2it.com/tveditorial/tve_main/1,1002,274%7C87709%7C1%7C,00.html |website=Zap2it |archive-url=https://web.archive.org/web/20040817070003/http://tv.zap2it.com/tveditorial/tve_main/1,1002,274%7C87709%7C1%7C,00.html |archive-date=2004-08-17 |quote=Along the way, the easygoing Archer has been forced to make difficult and sometimes-questionable decisions, all of which have taken their toll. |url-status=dead}}</ref>

While on his mission to locate the Xindi, Archer is briefly [[Extinction (Star Trek: Enterprise)|transformed]] into a member of the extinct Loque'eque by a mutagenic virus. Later, he is infected by [[subspace (Star Trek)|subspace]] [[Parasitism|parasite]]s, creating an [[Twilight (Star Trek: Enterprise)|alternate timeline]] in which the ''[[Enterprise (NX-01)|Enterprise]]''<nowiki/>'s mission fails and the Xindi succeed in destroying Earth (although the nature of these parasites mean that this timeline is erased when Phlox's cure for Archer erases the parasites themselves from history). With the help of [[List of minor recurring characters in Star Trek: Enterprise#Daniels|Daniels]], Archer, along with [[T'Pol]], [[Carpenter Street (Star Trek: Enterprise)|travels back in time]] to the year 2004 to prevent the release of a Xindi-Reptilian [[biological warfare|bio-weapon]].

By the end of the season, Archer is [[Zero Hour (Star Trek: Enterprise)|presumed dead]] when the Xindi superweapon is destroyed, after having convinced three of the five Xindi races that reports of humanity's future conflict with them are wrong. However, in reality, he is transported back to the early 1940s during [[World War II]], as is the ''Enterprise''.