Driven by her resolve to erase the Spirit of Origin from existence, Kurumi is fighting a battle of her own. And at long last, the identity of Phantom is revealed.

Shido is shocked when Mio tells him that all the Spirits are dead. Stunned and unable to move, Mio nearly wipes his memories as Shido, but there is still one Spirit who's survived.

Kurumi manages to survive Mio's assault and the other Spirits arrive to aid Shido. Realizing why he failed to seal Mio previously, Shido plans to kiss her again and this time make her choose him over Shinji.

Shido returns to a time before the final battle with DEM began, when no one has died yet. In order to avoid repeating the same future, Shido asks Reine out on a date. After hearing the story from Shido, Kotori and the Spirits support their date.

As Shido's date with Reine is winding down, Reine comes to the realization that history has been rewritten. With DEM approaching, Kurumi arrives at their location to aid Shido.

While Shido and Mio face each other and convey their feelings, Westcott activates his terrifying ritual. Can Shido and the others stop his plot from achieving fruition?

As the score results for the annual contest comes in, even though Miku won the best performance, the support of Raizen's Maid Café earns Shido enough declare winner. Depress and refusing to accept Shiori's friendship, Miku unleashes her angel Solo brainwashing the crowd, except Tohka, and hold down Shiori. But then Miku finds out Shiori is a guy leading her totally shock. To make matters worse, Fraxinus and Kotori fallen under Miku's control too, and Ellen abducts Tohka. Shido manages to escape, however, he is now a fugitive in the city. Thought-out the disturbance, Shido meets Kurumi and begs her to help him. Tohka awakens in the DEM facility restrained.

A certain time, a certain place. Shinji Takamiya encounters a spatial earthquake, but finds a girl at the scene. She remembers almost nothing about herself. Shinji gives her the name Mio and she goes to live with him and his younger sister, Mana.

Shido is flooded with memories as the girl named Mio Takamiya stands before him. She was the person with whom Shido once shared his feelings when he was Shinji Takamiya. Meanwhile, Kotori and the others learn of Reine's true identity.

Shido takes charge during their Valentine's Day date and trusts his gut to capture Kurumi's heart. Before it ends, a look into Kurumi's past sheds light on how she became a Spirit.

Origami is on a mission to avenge her parents, but when she finally discovers the truth, it turns out to be much harsher than she bargained for.

Shido wakes up by the troubles of both Tohka and Yoshino and somehow resolves it, meanwhile Origami got suspended for two months by the AST. While eating their breakfast, Shido receives a text from Origami and they discuss about the event that happened a month ago, While cleaning the room of Shido, Tohka notice a suitcase (for their school-trip) that is a resemblance of a drama sequel on the television. Tohka got worried and rushes to find Shido with Origami. While Shido tries to make it up with Tohka by getting her some kinako bread on the way home he notices that the lock of his suitcase was broken, so he went out to meet up with Origami again. While Tohka imagines another scheme of the show she rushes again to find Shido. And this time he caught Shido and Origami together and imagines that Shido is abandoning her for Origami. Tohka gets jealous gaining some of her powers and runs off while carrying Shido's suitcase. Elsewhere, Tohka's unsealed power starts to create a spacequake. Shido rushes to find Tohka and finds her in their special place and Tohka (misunderstanding everything) tries to prevent Shido from leaving but he explains that all is a misunderstanding, while Tohka cannot control her powers and hit Shido with shockwaves but Shido manages to seals Tohka's power again. While Isaac and Ellen are scheming a plan for Tohka, meanwhile Kurumi plots to kill the first spirit.

The woman stalking Tohka and Shido before, Ellen, finally reveals her true colors and orders a pack of mechs called Bandersnatch units after Tohka in an attempt to capture her. During the clash, Tohka gets incapacitated and captured only for Shido to call upon her sword to break the Bandersnatch off her. Meanwhile, Kannazuki and his crew on board the Fraxinus gets attacked by an enemy airship. Kannazuki launches a counterattack after deflecting several shots, leading to a full-scale dogfight between the two ships. Back at Shido's battle, Ellen falls down into a pit trap (oddly enough) dug by Ai, Mai, and Mii allowing Shido and Tohka to escape. Running to Kaguya and Yuzuru, he summons Tohka's power to intervene the duel and convinces both the girls to forget about becoming Yamai and focus on enjoying their lives together. Noticing the airship that attacked the Fraxinus, the twins combine their powers and eviscerate the ship with one massive blast. After the incident, Shido successfully seals the Yamai twins' powers, unfortunately stripping them of their clothes just as Tohka arrives. Meanwhile, Kotori learns from a strange man that Shido has manifested a spirit's power and that she might have to kill Shido if the situation worsens.

Shido and Kurumi arrive back at the Tengu Square to reason with Miku. Obnoxious she attempts to assault Shido, but Kurumi's power intercepts as she's resistible to Miku. As Kurumi distracts Kaguya, Yuzuru, and Yoshino; Kurumi traps Miku with Shido in a dark void to have private conversation. Despite his apology she still will not listen, so Shido makes his way to rescue Tohka alone. Westcott torments Tohka for his ambition to harness her power in despair. Fake spatial quake alarms are set off to evacuate all civilians. Kurumi holds off a pack of Bandersnatch units, as Mana appears and everyone aboard Fraxinus are back in their right minds. Meanwhile, Miku struggles about Shido's justice whether he actually cares for others than himself. Infiltrating the DEM Industries, Mana and Jessica engage, communications are jammed, Shido summons the Sandalphon to swipe the guards and enduring Kotori's healing ability.

On a mission to avert disaster, Shido attempts to rewrite history. Can he stop Origami's crazed rampage or are her parents doomed to die?

A full-scale confrontation between Shido and his friends Ratatoskr and DEM has begun. Kurumi and her clone, AST led by Ryoko Kusabe, join them, and as the battle intensifies, Shido confronts a horde of pseudo-Spirits, Nibeelcole.

Shido and the others face off against "Nightmare", and they receive some unexpected help.

Shido wakes up and finds that the world around him is different. His attempt to thwart disaster may have succeeded, but for how long will it last?

Shido takes Origami on a date but she's not acting like herself. After all hell breaks loose, the fate of the world depends on whether he can reach out to her heart or not.

Kotori and the others gathered on the bridge of Fraxinus learn that Kurumi has traveled back in time 204 times to try to save Shido. Shido also tries to search his memories to learn who Mio Takamiya is, but...

As Shido rushes to the Spirits' side, Westcott blocks his path. Meanwhile, Tohka and the others find themselves overwhelmed and powerless before Mio's manifested Angel, Ein Sof Ohr.

Many spirits were exhausted by Mio's Ein Sof Ohr and collapsed. Kotori directs Fraxinus toward Mio and fires her spirit cannon, Gungnir, but...

While the witch impersonates one of his friends, Shido is forced into a game where he must identify Natsumi before it's too late and they all disappear.

The suspension placed on Origami is finally lifted, we see Kusakabe having some complaints and a new character is introduced into the series. Shido is selected as the organizer of the Ten-Oh Festival, after a spacequake alarm goes off, Shido gets working and a new spirit is revealed, Diva, proves to be more of a challenge than the other spirits. AST interrupts Diva and they go on trying to take her down resulting in her escaping, after Shido encounters himself in a troublesome situation. The transformation of Shido into Shiori begins. The fierce battle to win Diva over begins, but will Shiori be able to accomplish the task at hand or will Diva be more challenging than expected?

Mana finally awakens from her battle with Kurumi. For the upcoming competition Ai, Mai, and Mii prepare a band to compete against Miku's. Origami hears from Ryōko about the usurp mission in capturing Tohka and Shido during the festival. Serving a Maid Café with the Yamai twins employed, Shido (as Shiori again) even hands out posters as the head maid when he and Miku come across and ask "her" to date her though Shiori still annoyed of Miku's arrogance. Shido then finds the bandmates were manipulated and will not perform for the concert. Fraxinus cuts the stage's power to slow things down, but Miku gets the advantage with her Astral Dress. The AST led by Jessica target the Tengu Square until Ryōko and Origami piloting the “White Licorice” interfere. Kaguya and Yuzuru as they are professional, backup Tohka and Shido to perform as best as they could regardless of outside interference.