As of 2409, Vega Colony is home to more than 2.8 million Federation citizens. The colony's administrator is Willa Post; other known current or former residents include Kolez, as well as Cpt. Va'Kel Shon and his family.
- “Assimilation of the Innocent”: The player has to warn Vega Colony of an impending Borg invasion. After the Borg start to assimilate Vega IX, the player has to fight them off while evacuating as many colonists, including Willa Post, as possible. Eventually, Vega Colony has to be abandoned to the Borg for the time being.
- “Khitomer Vortex”: Via a time vortex in the Quadra Sigma System, the Borg travel back in time to influence the events which have taken place during their initial assimilation of Vega Colony.
- “Khitomer in Stasis”: In an underground facility on Vega IX, the players must destroy the time-travelling Borg's capacity to upgrade the older drones which had been dormant below the Vega Colony.
- Although the canonical location of Vega (Alpha Lyrae) on a 2D-projected galaxy map would be in the Alpha Quadrant, at the border between the Denobula- and Tellar Sectors, Star Trek Online puts it in the Risa Sector. This misplacement was a conscious decision, in order to simplify travel from Vega to the Pollux System for fresh players of the Federation tutorial.
- Vega IX and the Federation tutorial missions taking place on and around it were completely revamped with Season Eight: The Sphere.