Hibiki Kuze, is waiting for his friend, Daichi Shijima, after finishing their practice exams. While discussing their future, Daichi introduces and registers them onto a recently popular website called "Nicaea", a video delivery site that allows people to see videos of their friend's death. Later, at the train station, they receive videos from Nicaea that show both of their deaths by an oncoming train at that exact station. Shortly after, before the train arrives, an earthquake occurs, causing the incoming train to derail and cause the same devastation they saw in the videos. On the verge of death, Nicaea offers Hibiki a second chance to live and a Demon Summoning App is forcefully downloaded into his phone. He and Daichi awake to find the station in ruins with most of the people dead. They then witness vile wolf-like creatures eating the corpses of the recently deceased.

Hibiki, Daichi and Io are arrested by the JPs and brought to a secret underground base located at the National Diet Building. Here, Commander Makoto Sako, explains to Hibiki that the JPs protects Japan from "paranormal anomalies" before she introduces the JP's Chief, Yamato Hotsuin who says that Hibiki's demon Avatar: Byakko is unique, being one of the four symbols of the Chinese constellations. Furthermore, he explains that the Dubhe was only one of 7 creatures called the Septentriones, each of which will appear in the next six days and should the JPs fail to defeat them then the world will disappear. As the JP's scientists begin to analyze the demon summoning app, Hibiki ponders on Yamato's words. The following day, Makoto releases them by taking them to an emergency shelter in Chūō. Here, it is discovered that a rumor of demons running amok is spreading. As Hikibi looks around at all of the refugees in a church, a winged-demon attacks and Hibiki summons Byakko to protect them.

Under Yamato's order, Hibiki, Daichi and Io rides on the secret train of JP's to Osaka to help find their chief scientist, Fumi Kanno, who has lost contact recently. They are greeted by another summoner of JP's, Hinako Kujou, at their arrival, but the other summoner Keita Wakui is less welcoming of the three fellow summoners and is returning to his mission of hunting down malignant demons. At the Osaka headquarter, its computer system is under attack from the whole Japan's network. At the same time, Hinako receives Keita's death clip, Hibiki instantly concludes that the scene of Keita's death is related to the hacker attack. Although Hibiki asks an operator to inform Keita not to head to the location of his death scene, Keita cannot receive the call due to being ambushed by Gozuki and Mezuki. All four summoners head to the abandoned theme park where the hacker attack originates from.

Following Keita's sudden death, Hibiki remains visibly shaken due to the fact that they couldn't prevent it. As Merak arrives in the city, Yamato has JP's members move Hibiki into position to intercept it. At the Osaka Juso Ohashi Bridge, the Japanese military tries and fails in their attack against Merak while Botis and "The Anguished One" discuss the state of affairs. With of the loss of most Osaka's spiritual barriers, Merak fully manifests itself and makes its way to the final barrier - "Tsutenkaku". Meanwhile, as Hibiki is deployed into the field, Hinako and Io discuss his mental state due to Keita's death. Meanwhile at the Umeda Sky Building, JP's summoners try to stop Merak with a swarm of Itsumade but it kills them all in an instant. As Io heads to Hibiki's location, Merak then launches a devastating ice attack, at the "Tsutenkaku" barrier, which survives, but the attack leaves a path of destruction and kills many more people, upsetting Hibiki.

Makato briefs an infiltration team of JP's agents on their way via train to retake the JP's Nagoya Branch from Ronaldo's control. At the same time, Daichi and Io stow away on the train and ponder why Hibiki left them behind. Just then, they are shocked to receive Hibiki's death clip and resolve to save him themselves since the only people able to receive death clips are friends. In the meantime, the JP's tries to reassess the situation after loosing contact with Hibiki and now their infiltration team as Dr. Kanno repairs the damage to the JP's Osaka servers. Meanwhile in Nagoya, Jungo Torii and Airi Ban plan to infiltrate the JP's Nagoya Branch and retake it from the insurgents, although Airi also speculates that the JP's and the Resistance (Insurgents) had prior knowledge of the calamity. Elsewhere, Daichi and Io arrive in Nagoya to discover a Resistance camp handing out rations to civilians. Just then the camp is attacked by a swarm of rogue Legion demons.

Airi and Jungo sneak into the JP's Nagoya Branch through the air ducts, while elsewhere, Daichi and Io rush to Hibiki's location in order to prevent his death. As Ronado, Hibiki, Joe and Otome scout the Nagoya TV Tower in anticipation of the third Septentrione, Otome is hesitant to fight, especially when the JP's members such as herself have been told little to nothing about the Septentriones, although Ronaldo states that they should have no problem since their demons are much stronger than those used by JP's summoners. At the same time, as Hibiki ponders on Nicaea's origin and his power. Later, back at the Nagoya Branch, Otome and Hibiki have a brief discussion comparing Yamato's methods versus Ronaldo's methods. At this time, Daichi and Io arrive and tell Hibiki about his death clip while Makoto covers for them at the JP's Headquarters. Daichi and Io try to get Hibiki to return with them but he states that he can't because of the imminent Septentrione attack.

As the exchange between Hibiki, Yamato and Alcor continues, Yamato rejects the notion of a person's fate being predetermined by the death-clips. As Hibiki is forced to make a choice of staying with the Resistance or returning to the JP's with Yamato, Ronaldo tries to sway his decision but is stopped by the demon Bifrons. As everyone realizes that Alcor isn't using a cell-phone to control the demon, his origins are questioned by Hibiki to which he responds that he genuinely doesn't know, only that he isn't their enemy. Ronaldo has the Resistance summoners surround him with demons, but Bifrons easily incinerates them. Alcor goes on to calmly reveal that he is the creator of Nicaea and the Demon Summoning App, which he gave to humans as a means to fight the Septentriones, finally remarking that it allowed him to find a new "Shining One" in Hibiki.

Hibiki and the rest of the summoners fights against Megrez that have appeared simultaneously in Tokyo, Osaka, and Nagoya. However, Megrez will continuously revived unless the three main bodies are defeated at the same time. As the battle starts, Hibiki and Io summons their demons, along with Hinako who uses Berserker to avenge Keita's death, while Yamato uses his power that increased by the Ryumyaku tower and his demon Baal to stop Megrez' movement until the right moment. During the battle, Hibiki and Io received Ronaldo, Joe, and Otome's death clip that shows them died by Megrez' attack. Hibiki immediately tells Ronaldo to escape, but Ronaldo, Joe, and Otome decides to keep fighting since there are no summoners other than them that can defeat Megrez and resolves to avoid their fate like Hibiki does yesterday.

Hibiki awakens on Thursday and to his surprise, finds Alcor waiting in his quarters. Over coffee they casually discuss the state of affairs. Hibiki, now believing that Alcor isn't a threat, gives him sanctuary in his JP's quarters, with a promise that he not reveal himself and what he actually is to anyone, for fear of creating a panic within JP's. Just then, Daichi and Io enter Hibiki's quarters and find Alcor, much to their shock. Although, Hibiki is forced to confide in them about Alcor's nature. Later that day, Airi and Hinako are selected by Makoto and Fumi to challenge the next Septentrione. Much to Hibiki's reluctance to let them fight, Makoto explains that the Septentrione: Alioth is scheduled to manifest in the Earth's Ionosphere, and hence, specialized long ranged demons that only Hinako and Airi can summon, stand any chance of attacking it.

The following morning Alcor surprises Hibiki, Daichi and Io by making breakfast for them, while Io withholds her fate from Hibiki and Daichi. Later, Alcor visits Yamato and expresses his concern over what consequences Io's death would have on Hibiki, although Yamato shows no sympathy for Alcor's anguish. Finally, Io is summoned by the JP's while Hibiki and co. are briefed on the Septentrione: Mizar's abilities of self-replication. As the group expresses concern on a battle plan, Yamato and Makoto reveal to their horror, Io inside a machine connected to the "Brionac" and their plan involving Io's sacrifice for Lugh. Furious, Hibiki demands another plan, although Yamato's logic trumps him. Finally Mizar manifests in Tokyo prompting Yamato to begin the summoning for Lugh. Simultaneously, Hibiki, Daichi and Hinako receive Io's death clip, causing Hibiki to storm out of the JP's headquarters.

Hibiki is put into intensive care at the JP's' Tokyo Branch. As the demon summoners look on, Io can't help but feel responsible for his current condition, although she is comforted by Jungo and Airi. Meanwhile, Alcor is visited by Botis and Bilfrons, the former of whom tries to attack him because of his supportive stance on the humans. Fumi updates the JP's phones with software capable of summoning stronger demons. The next day, Io, Daichi, Airi, Jungo and Hinako have breakfast together in a single moment of peace and officially introduce themselves to each other. As they go to exchange emails, they all simultaneously receive each other's death clips. Suddenly the last Septentrione: Benetnasch appears and destroys the Sapporo barrier with a single attack allowing the Void to consume the region. As Fumi outlines that it possesses the abilities of its predecessors, the Osaka and Nagoya regions are wiped out each with a single blast. Yamato then orders everyone to begin the operation.

With the Trials of Polaris behind them, Alcor appears before Hibiki and co. and states that he intends on killing Yamato of his own free will and in doing so, entrusting the fate of the world to Hibiki, a battle which Yamato accepts. As their battle begins, Hibiki explains to Daichi and Io what would happen to the world if Yamato has his way after meeting with Polaris. While attacking Yamato with tentacles, Alcor realizes that Yamato had been steadily drawing him closer to the Tokyo Tower to enhance his use of the Ryumyaku. Afterwards, they take a short pause and exchange threats. Alcor expresses his support of Hibiki's future since he was treated as an actual person when with him, although Yamato retorts that Alcor should revert to being a mindless tool, and if so, he would be allowed to see his vision of the future. Just then, they both receive each other's death clips. Hibiki also receives their death clips and decides to keep his promise to Yamato by stopping him.

Not having anymore hesitation to fight, Hibiki reminds Yamato of their promise of defeating him and having an audience with Polaris. As their battle begins, Yamato notes that Hibiki is driven by his anger towards him and his warped reasoning behind sacrificing the lives of everyone. Although, Hibiki defends by stating that as a human, he cannot allow such injustice to prevail, causing Yamato to question his own humanity. As Hibiki defends an attack using Shakko's power, Yamato acknowledges him as an equal and reveals that their current situation had all been part of a grand scheme put into motion by Polaris since the moment of their births. However since Polaris itself is flawed by its own nature, it had left it up to humanity to decide amongst themselves who should survive until the end, whilst citing the anomaly of Alcor's nature as proof of this. This truth shocks Hibiki, but Yamato simply brushes it off as semantics in his goal to reshape the world into a meritocracy.