The title comes from Valen's final recorded words on Babylon 4, as preserved in the DC Comics series In Valen's Name. The game builds its story around that phrase and the question of what Valen was still searching for at the end of his life.
The main story begins five years after the Earth-Minbari War. Earthforce is struggling to reassert control over trade routes now overrun by well-organized, heavily armed raider groups. Commander Richard Kelly — a twelve-year veteran of the Minbari War — is assigned to lead Alpha Squadron aboard the EAS Perseus, an Omega-class destroyer, to restore order in the remote Neutral Sector 318. Kelly survived the war without ever engaging a Minbari warship directly, but the fear those years instilled has never entirely left him.
Behind the present-day mission lies a history stretching back a thousand years: to Valen and the Shadow Uprising, and to the companions who followed him — Rashok of the Warrior Caste, Nukenn of the Religious Caste, the eccentric and singular Zathras, the banished Ramde Zarwin of Tak'Cha, the outcast Virenna, and the warrior Sinevar. One by one, those companions died or departed, until only Nukenn and Sinevar remained at Valen's side. When Sinevar failed to return from a deep-space journey, Valen's wandering ceased entirely. He stopped searching. And then, at the end, those final words.