The Atlas was the flagship of the task force assigned to intercept the fleet of ten Borg cubes before they could assimilate Vulcan, Bajor, and eventually, Earth. When the Borg arrived at the outskirts of the Vulcan system, the Atlas engaged the enemy using transphasic torpedoes, beginning the Battle of Vulcan. Bateson's ship was eventually able to destroy several cubes before the Borg could finally adapt to the weapon and started their counterstrike.
Most of the task force was destroyed, but the heavily-damaged Atlas managed to outmaneuver the Borg. When the collective started to fall into chaos due to Captain Erika Hernandez's link to the hive, the last Borg ships started to attack each other. The few that survived the fire exchange were destroyed by the Atlas, along with the surviving Federation ships, and Vulcan was saved again.
Following the invasion, the Atlas reported to Starbase 22, where station's counselor, Brian Ellis, counselled the Atlas medical staff.
In March 2384, the Atlas was at Orion, in the Pi-3 Orionis system, while a secret summit between the Federation and the Gorn Hegemony was being held in the secure sub-levels of the Bank of Orion.