After an unending war with the metastreumonic Force, the powerful organization Secreta Secretorum you belong to is finally ready to undermine the head-strong federation, despite an intense struggle for power.
The character the player embodies wakes up in a strange cave under the New Eden megalopolis after a fight and saw his fellow teammates die. He still remembers he's a member of the weird secret society E.Y.E, itself an armed branch of the Secreta Sectretorum. This last one will attempt a coup against the all-powerful Federation, a coalition of several worlds and planets ruling with an iron fist.