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During the Second Great War, the Aeneas was among the ships Valerian Mengsk took with him to assault Char. The assault that followed was met by heavy zerg resistance and while the Queen of Blades was successfully de-infested on the surface, the space battle continued as the zerg continued to attack the terran ships. Despite this, the Aeneas remained operational.
Events came to a head when the other half of the Dominion Fleet arrived, led by Arcturus Mengsk himself. Mengsk demanded that Valerian turn Kerrigan over for termination. Valerian refused, and the two halves of the fleet engaged in battle as a result. In the exchange that followed, the Aeneas was immobilized, left to drift in space.
The ship was likely named after the mythological hero of the same name.