At the outbreak of the Great War, Gantrithor was the flagship of the Koprulu Expeditionary Force sent to prevent the Zerg Swarm from gaining a hold in the Koprulu sector. In the first months, it participated in the purification of the terran worlds of Chau Sara, Mar Sara and Antiga Prime. The campaign failed at Tarsonis and the fleet was recalled to Aiur. Tassadar refused to return and took the carrier alone to Char to investigate a psionic call from an unknown entity.
Raynor's Raiders and the Terran Dominion's Alpha Squadron were already investigating Char for the same reason. When Gantrithor arrived the terrans were already under attack by zerg boarders. The super carrier destroyed every terran ship regardless of affiliation to stem the infestation. Only the terran flagships, Hyperion and Norad III, escaped.
Tassadar's disobedience rankled the Conclave and they dispatched Judicator Aldaris, Artanis and the Fleet of the Executor to find him. Artanis joined forces with his predecessor at Char and Gantrithor joined the fleet. Together they returned to Aiur.
Gantrithor went into battle one last time at the end of the Great War. With Tassadar in command it joined a combined protoss and terran assault against the Overmind. To ensure the creature's destruction, Tassadar ordered the carrier on a collision course with the Overmind, while he channelled the energies of the Void for the killing blow. Gantrithor was pursued by mutalisks and guardians. Several mutalisks entered the interior and caused significant damage. The energies erupting from Tassadar's body were too great for the ship; the carrier burst apart, releasing a coruscating bolt that destroyed the Overmind.
The Gantrithor is only controllable in "Eye of the Storm". It functions as a hero unit.