Deveneaux meets with and reports to the newly-branded Phoenix Council. Meanwhile, a name from Castro’s past gives him hope for the future.

Castro returns to the surface - alone - to get closer to Cutty and Bath's simulacra. The Shadow Council rebrands itself and revises some policies to quell dissent.

Cutty struggles to reconcile Colonel Marsh's sudden change in attitude about his role in the mission to the surface. Castro returns to the surface, intent on escaping Nut Island - but first he must survive bizarre and violent obstacles standing in his path.

Castro's research into the team's past reveals a shocking truth about Ghaniyah. Bath seeks company from Harumi Gale, who is hiding a secret from her mentor. Cutty's investigation into the rousting of the squalor is stopped short by an impatient Colonel Dana Marsh.

The situation deteriorates as tensions boil over in the Phoenix Project. The team learns that the green stream technology may be more than it seems.

Bath and Cutty make plans for their next move. Hostilities on the surface mirror  conflict in the Phoenix Project.

Major Cutty and Dr. Bath get to know Kick and his family. General Castro meets a mutant on Nut Island.

After fleeing from an attack on the Ferry, the Phoenix explorers find themselves confronted with another group of locals and must decide whether to offer aid in a critical situation.

Bath turns to an old mentor for advice. The reunited team returns to the surface and receives a hostile welcome.

Doctor Chang sets out to repair the fallen simulacrum. Castro and Cutty address the security of the facility on Liberty Island.

Jon Bath helps his friend Mike with a personal problem. Doctor Chang makes her first foray to the surface.

General Castro and Major Cutty prepare to move on without Dr. Bath's Simulacrum.  Dr. Bath and Dr. Ghaniyah discuss life in the Phoenix Project.  Danielle Deveneaux presents a proposal to the Shadow Council.

Professor Bath finds himself lost in the Greenstream when his simulacrum is disabled in a fight. Doctors Ghaniyah and Chang try to find a way to free his mind without permanent injury.

The Phoenix team learns about the environment on Liberty Island. Danger surfaces when they realize they may not be alone.

In their robot bodies, the Phoenix Project explorers take their first tentative steps on the surface of Earth. Doctor Chang and Doctor Ghaniyah discuss contingency plans.

The group has concerns as they prepare to transmit their minds into artificial bodies on the surface for their first mission. Major Cutty considers his past relationships and questions what he has been told.

The team of explorers from the Phoenix Project learn more about each other and about the missions to come. Doctor John Bath considers his role in the project and Danielle Deveneaux discusses her assessment of the team with her enigmatic superiors.

In the year 2112, General Binyamin Castro is awoken from cryostasis in the underground Phoenix Project deep beneath a war scarred, post apocalyptic Earth. He has been chosen to lead a team consisting of scientist Dr. John Bath, soldier Major Leonard McGuillicutty and other members of the Phoenix Project to determine whether the surface is ready for humanity to return from their decades long exile and reclaim their rightful home under the open sky.