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.
ARKS pays a great price in withstanding Elder's attack. As Theodor searches for Ulku, Echo fears for Zeno while pretending to remain strong. And distraught from losing Gettemhult, Melfonseana...
Having believed [Elder] was destroyed, Ash is deeply troubled after learning he still lives. Meanwhile, the search for Zeno on Naverius is called off after ARKS on the planet are slaughtered by a rampaging dragon.
While searching for Zeno on Naverius, tales from an old man living in some ruins help Ash get closer to the truth of the ARKS-eating rampaging dragon which Quna is still trying to locate.
Ash and Afin are sent on a mission to investigate Planet Wopal. There they reunite with Echo, who has been throwing herself into battle with newfound determination.
Ash decides to cooperate with Xiao in order to thwart Luther's ambitions. After Ash is shown remnants of Luther's experiments, Xiao tells him about Luther's goals and explains how Xion is the key.
Out of nowhere, all ARKS are ordered to return to the fleet. What's more, a certain rumor has spread through the panicking ranks of ARKS. Xion appears before a troubled Ash and says this is the moment they have been waiting for.
Guided by Xion, Ash and Matoi head towards the core of the Mothership but find that their way is blocked by the strongest defenders of ARKS.
Gaining the cooperation of the Council of Six, Ash and Matoi rush onwards to save Xion. But before they can reach her, standing in their way is...
Fueled by rage, Luther unleashes the form of Dark Falz [Luther] and attacks Ash. To stand a chance against [Luther]'s overwhelming power, ARKS must unite and confront him together. How will the battle end?
Ash learns from Xiao that all data regarding Matoi and a certain incident ten years ago was completely erased from Xion's memories. Ash resolves to go against the time stream to uncover the truth, but waiting for him there is…
Driven by a thirst for revenge, [Apprentice] assaults an ARKS Ship. With Klariskrays the Second separated from Clarissa, [Apprentice] employs despicable methods to corner her. Ash rushes to her side in hopes of saving her, but…
Ash returns after seeing what fate befalls Klariskrays the Second with his own eyes. Meanwhile, following his encounter with [Apprentice], Afin attempts an investigation of his own to learn more about Dark Falz.
A Falspawn attack on Lillipa prompts an emergency call to arms. Thinking that [Apprentice] may appear, Ash and friends head there at once. While helping Afin search for Euclyta, Melfonseana struggles with her emotions when suddenly reunited with [Elder].
Ash and Matoi have a surprise run in with Sarah who gets frazzled and scurries away at the sight of Matoi. While trying to chase her down, Ash encounters Maria and learns about the "sin" which heavily weighs on Sarah's shoulders.
Ash finally discovers the true identity of the masked Dark Falz who stabbed Matoi. Confronted with the fate of Matoi as well as his own, Ash broods over how he might save her while making his way to visit a certain someone.
Trapped within [Gemini], Ash and Matoi once again meet Luther the Fallen who has become a part of [Gemini]. There he reveals the truth behind the void in Ash's memories.
The [Profound Darkness] has revived. Desperate to defeat it whatever the cost, Regius and Xiao make a heartless decision. However, Ash holds Matoi too dearly to sit back and do nothing.
The final battle begins. As the entirety of ARKS unites as one in hopes of saving Matoi, Ash confronts her now that she's finally become the [Profound Darkness].