During the rebellion of Captain Hikaru Sulu and the ISS Excelsior, which in actuality was Captain Sulu and USS Excelsior crew from the "primary" universe, the Phobos was dispatched along with the Miranda-class ISS Brigand and ISS Enterprise to apprehend the Excelsior before she could leave Terran space.
The three starships confronted Excelsior at an abandoned starbase in the Epsilon Indi star system. The Brigand and Phobos engaged the Excelsior first, in order to prevent her from obtaining the dilithium crystals needed to repair her warp drive. As the battle played out, the Brigand was destroyed with all hands aboard by Imperial Spectre-class fighters from the Excelsior, which used a combination of hit-and run tactics, as well as close quarters attacks out her phaser and torpedo aim. The ISS Enterprise assumed the Brigand's position and continued to barrage Excelsior. (TOS video game: Shattered Universe)