On his first day as a member of ARKS, Ash, a man on a journey of self-discovery that is plagued by a recurring dream of a woman that speaks of fate, is recruited into the Oribe Unit where he meets a fellow comrade named Afin, whom insists on calling him "partner." The two find themselves in a dangerous situation when the unit is ambushed by falspawn and slaughtered. Able to escape with the help of experienced ARKS members, Zeno and Echo, the group comes across a mysterious white-haired girl and an even more mysterious masked man intent on killing her.

Though many perish, Ash and Afin return safely from their training. However, their first mission as new ARKS is to return to Naverius with their commander Kohana and the mysterious girl Matoi, and exterminate the rampant Falspawn.

During a mission on planet Naverius, Ash learns about the battle between ARKS and Dark Falz after encountering a girl on the "Council of Six" -- The six most powerful ARKS in the entire organization.

Back on an ARKS Ship, Ash and company are taking a breather when they meet Ulku, a girl who yearns to join ARKS. She talks about her childhood friend who joined ARKS without her and how he might be in the same class as them.

ARKS Ship 128, the "Themis", is attacked by Falspawn--the first such incident in 10 years. The ARKS soldiers can’t hide their panic as they sortie. Meanwhile, as Zig labors to repair the weapon...

Ash reunites with Zeno and Echo on his way to the medical center to visit Matoi. He finds her well, but his relief is cut short when Gettemhult shows up out of nowhere.

His revival successful, Dark Falz Elder assaults the Oracle fleet. Desperate to defend the fleet and the universe, ARKS takes a stand against his dreadful power.