Jax, the protagonist, is an Alb Commander on a special mission. His aircraft is shot down by an unknown enemy and then crashes over a mountain. He is knocked out for days, in which time most of the Elex clears out of his body, leaving him weak and alone in an unknown location and with a now-free mind. He tries to find out what happened to him and who attacked him. In doing so, he gets involved in the larger problems troubling the inhabitants of Magalan. A key mechanic is whether the player decides to be a cold person (logical and practical) who keeps his Alb personality and goals, or more emotional, by showing passion and helping the Free People for more ideological and altruistic reasons.
In exploring the world, Jax discovers through audio logs and old documents that the pre-impact government had predicted the comet's impact and secretly commissioned a project called Operation Calaan. This project, under the leadership of a Dr. Dawkins, sought to prevent extinction by taking a select number of people into space on a rocket nicknamed "Calaan". The rocket since became mythologized as a deity by the Clerics, who are unaware of its true nature. The operation failed due to mismanagement and general panic, and the rocket never launched.
After gaining allies, resolving inter-faction conflicts and beating back the Alb invasion, Jax finally confronts the Hybrid. He discovers that the Hybrid is actually the former Dr. Dawkins. He had sealed himself in a protective chamber and survived the blast itself, but was affected by the Elex. A mysterious and highly advanced alien species spoke to him through the Elex and told him to prepare the world for their arrival. He and his chosen Albs thus sought to find and consume all Elex at all costs so that they may "evolve" and be allowed to survive.
Eventually Jax manages to defeat the Hybrid. Before doing so however, the Hybrid is able to send an unknown signal into space. A strange, large shape appears in the sky as Jax resolves to prepare the world for the arrival of the aliens.