Ten years have passed since the creation of the Lightless Realm, and the city of Kukujicho becomes more desolate as people's fears increase. Akashi Saginuma, an elite student attending Kukunochi Academy, gets called out by his teacher along with his amiable friend, Iwato Namito. There, they are informed of a "pilot training course" that only the most outstanding of students become selected for.

"Those who hear the Corpse's song will die a mysterious death within nine days." As if that rumor became truth, an incident happened before Akashi and his class. Emiru and Mahmu head over to the ruins of a hospital in order to confirm the other rumor that "the Reaper" -- something that supposedly can defeat the Corpse -- was dormant there. And there, they meet Heito Isaku, another one who was chosen to be part of the pilot training course.

"The Reaper" was something created in order to defeat the Corpse. Akashi starts training as the pilot for "the Reaper," but with excessive stress, he cannot hide his mounting frustration. Meanwhile, Sasame Izuriha, the last of the pilot candidates, finally transfers into class. Akashi finds that Sasame is somehow on his mind and tries to talk to her...

Akashi and the pilot candidates were dropped down onto a deserted island for mock investigation training in uncharted territory. While one condition for them to clear the mission was for "all members to gather in one location," Iwato and Raika fear the danger that Heito, who landed on the deserted island earlier than the others, possesses. While the candidates are enveloped in anxiety and terror beyond words, it was Sasame's singing voice that guided Akashi and the others.

Synchronization of thought between the pilots is necessary to control a MA-Vess... Heito and Emiru, showing high synchronicity, are involuntarily paired up for field training near the Lightless Realm. However, as if it was reacting to the terror Emiru hides deep within her heart, the environment becomes surrounded by an abnormal atmosphere. Over time, Heito's insanity corners Emiru, forcing a situation where there was no turning back from.

Everyone including Akashi was enveloped in deep sadness about the worst-case scenario that descended on Emiru. As if feelings the pilot candidates had like those were being ignored, they were ordered to go on 24-hour standby for security reasons. While Minashi, who disobeyed the standby orders, and Heito, whose mind was fixated on Emiru, were heading to the laboratory, an unexpected enemy assaults the academy. Akashi, moved forward by Emiru's wishes, boards the Reaper and sallies forth.

The fact that the Corpse appeared outside of the Lightless Realm threw the entire academy into terror. While rushing their efforts to get the next prototype based on the Reaper into combat, they started selection for its pilot; and there, Natsuiri comes up with a certain plan. One night, Akashi visits the ruins of a town at Kasane's request, but the person who awaited was Heito. The case involving Emiru has Heito's hatred of Akashi showing openly, leading to his incessant taunting of Akashi...

A signal from a data recorder that an investigative unit left behind in an area that was engulfed by the Lightless Realm ten years ago had been received. It was that of the unit that Aoshi had once piloted. Harboring complicated emotions, Akashi heads to recover the recorder together with Heito. As soon as they enter the Lightless Realm, the two lose sight of each other. Immersed in abnormal levels of tension, Akashi and Heito eventually come to cross paths with their pasts.

Akashi escapes from the Lightless Realm. However, Heito and the second machine, Sable, are left behind in the Lightless Realm with no idea whether they are still safe or not. Akashi tries to leave IX saying that he will never pilot the Reaper again, but when he randomly drops by the hangar, Natsuiri calls him back. Natsuiri, intent on the recovery of the second machine, starts to talk about a certain system that is aboard the MA-Vesses.

Akashi, finding out the secret behind the Reaper that he pilots as well as the second machine piloted by Heito, quietly decides for himself to rere-enter the Lightless Realm. As Akashi does his best to continue the search despite the encroachment on his psyche as well as the confusion caused by Aoshi's memories blending in, the Admonition attacks him yet again. After much painstaking effort, Akashi finally finds the second machine, but...

After Akashi's return, iwato and the other students were told of the second machine's grave secrets after grilling Natsuiri. Not heeding the anger felt by the students after hearing the cruel truth, Natsuiri proceeds to act in an even more surprising way. However, given the possibility of resolving a certain situation, Akashi becomes determined to defeat the Corpse no matter what. As he trembles in regret and anger, Akashi bumps into Sasame at a moonlit wooden terrace.

Sasame was praying for the safety of Akashi, who headed into the Lightless Realm. The original objective was the recovery of the second machine and Heito, but being so intent on protecting Sasame, Akashi continued to attack the Corpse, which had appeared. However, the Corpse's fierce attacks pushed the Reaper back and severely damaged it. Sasame, feeling the situation at hand, and with encouragement from Minashi's words...

The pilot of Gueules, the third MA-Vess that saved Akashi from his crisis, was Minashi Maki. Akashi becomes stricken with grief over reality of what the true identity of this MA-Vess is. As if he was taking out all his anger that now has nowhere to disperse to, he starts retaliating against the Corpse. Akashi and the Reaper mercilessly corners the Corpse, but then, one girl shows herself...

While the Lightless Realm continues to expand, the whereabouts of Akashi Saginuma remain unknown. Iwato and the other students left behind find out that they are known as the “children spirited away”. As the reasons why they were gathered together become more apparent, Mahmu decides to pilot Sable, the second machine, in order to grant Emiru's wishes.

Akashi, Tsugumi, and the Gargouille members had all met one another when they were young. The memories of the past that Tsugumi shared with them clearly showed the reason why the Lightless Realm was created. Meanwhile, due to the activation of the Lightless Realm, IX headquarters also faces an attack from Admonitions. Natsuiri is assaulted as well. Raika and Iwato head out on Vesses to protect the place that Akashi and the others can return to, and do their best to fight; however...

Akashi remembers the sin he had committed once upon a time in the Lightless Realm. Tsugumi's intent was to seek revenge against the eight children, including Akashi. The Corpse has now revived and starts to overpower Mahmu and Minashi with Tsugumi's anger and insanity. Akashi rushes over to the Argent in order to stand up against the Corpse. The roar of the Reaper echoes alongside his strong desire to seek salvation for Sasame.

To research the secret of the Arbornine that prevents the Necrometal infection from spreading, Suzaki, Akashi and the others secretly headed over to Yomijima, the island where Minashi and the two girls were born. The memories of the massacre that happened in the now ruined IX laboratory flooded into Minashi. Just then, Natsuiri, who had chased the group to the island, shows up together with the "very first MA-Vess.”

Controlling the MA-Vess loaded with Mimei, Natsuiri fends off the Admonitions created by the regrets of the islanders. However, Necrometal starts to slowly eat away at his body. Meanwhile, Akashi's group, seeking escape from Yomijima, becomes reunited with the stray Minashi at the back end of a small, old shrine on the island...

The right to command Akashi and company after their return from Yomijima was handed off to Suzaki. Kasane, who wants to solve the mystery behind the Lightless Stone, heads to the abandoned hospital in search of materials left behind by Natsuiri. However, during her search, an Admonition attacks. Akashi heads to rescue her aboard the Argent, but Kasane could feel nothing but uneasiness at its unnatural resonance rates.

Controlling the MA-Vess loaded with Mimei, Natsuiri fends off the Admonitions created by the regrets of the islanders. However, Necrometal starts to slowly eat away at his body. Meanwhile, Akashi's group, seeking escape from Yomijima, becomes reunited with the stray Minashi at the back end of a small, old shrine on the island...

Minashi alone defies orders and goes on ahead. He arrives at the Corpse in order to give Tsugumi some consolation, but Tsugumi interrupts him and lashes out in anger. The rapidly expanding Lightless Realm envelops even the IX tower that Kasane and Suzaki are in. While Mahmu keeps the Corpse's attention on herself at the front line, Akashi was hearing Heito's voice calling out to him.