Ambition of the Illuminus picks right up where the story left off in Phantasy Star Universe.

Shortly after the defeat of Magashi and the Endrum Collective, a mysterious group known as the Illuminus have appeared and threaten to exterminate all non-human races. The GUARDIANS themselves are under attack, and Ethan Waber is now wanted for an attempted assassination. Determined to find Ethan at any cost is GUARDIAN instructor Laia Martinez. As a new GUARDIAN receiving guidance from Laia, the player must search for Ethan and uncover the truth.

A new series of online chapters introduced by the expansion, having completed their training and become full-fledged GUARDIANS, players take the reins as instructors, passing on their knowledge to younger recruits while investigating the evil Illuminus organization. In addition, all of Episode 2 is available in the offline Story Mode on the PC and PlayStation 2 versions of the game and limited edition collectibles are given away as mission rewards, and some are given to your character at the beginning of the game.