Jonathan Archer was the Human Captain of the NX-Enterprise from its launch in 2151 until it was decommissioned in 2161. During this time, Archer played pivotal roles in the Earth-Xindi Conflict, the Temporal Cold War and the founding of the United Federation of Planets.
- “The Measure of Morality (Part 2)”: Captain Archer (or a simulacrum of him) commands the Enterprise against a rogue Excalbian Borg Queen simulacrum.
- “The Temporal Front” (Mentioned): After the player and Starfleet allies from the 29th Century prevent further Na'kuhl temporal incursions and destroy their temporal portal, Captain Benjamin Walker of the U.S.S. Pastak informs them of a new temporal record regarding the defeat of Na'kuhl leader Vosk by Jonathan Archer.
- Archer's dialogue in "Measure of Morality (Part 2)" are pre-recorded voice lines from Star Trek: Enterprise.