Season 2

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.

After a very awkward moment in Shido's class where Tohka tries switching genders in an effort to bunk with Shido, the class goes on a field trip to Arubi Island. During the entire trip, Origami and Tohka end up constantly annoying Shido in an effort to win his affections. Meanwhile DEM Industries, an organization with an interest in spirits begins stalking Tohka. Some time later, a massive hurricane appears out of nowhere while Shido and Tohka are on a stroll. Three trash cans strike Tohka, knocking her out in the process while two spirits viciously battle overhead. When Shido tries to intervene, the twin spirits Yuzuru and Kaguya decide that their next battle will be over winning Shido's heart to the latter's dismay. When the two girls follow Shido back to the class holding his arms, Origami becomes enraged over her new competition. As Shido's teacher tries to arrange the girls to be students in the class, Kaguya and Yuzuru explain that they were once one spirit named Yamai and that their contests are in an effort to find out whose personality will stay when the girls fuse and become Yamai once more. Later that day, an incident occurs when the twins drag Shido into the men's bath in an effort to sexually seduce him. Things get worse when Tohka shows up along with the rest of the class.

The twin spirits, still trying to seduce Shido, start cuddling up to Shido completely naked in bed. The situation worsens when one of his teachers walks in on the mess. Later, Shido plans to seal the Yamai twins' powers without letting one of them win in an effort to avoid both the unpredictability of the loser and what would happen to the loser's personality. During their contest, they have Shido coat their backs in suntan lotion ending up turned on from the application. Later, the Yamai sisters team up with Shido to take on Tohka and Origami in a volleyball game in which the winner is the former's team. During the afternoon, Origami is ambushed by a strange mech-like being.

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.

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.

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.

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.

Shido almost got caught until Miku makes an entry as she commands the Spirits to join the battlefield just to collect Tohka. Origami in a convention suit partners with Mana. While Shido and Miku argue, he reveals that Kurumi learned how Miku acquire her Spirit power from Phantom (like Kotori), she finally tells that she used to be a splendid singer Tsukino Yoimachi, but one day she rejected a TV producer's career offer due to disgrace, then bad rumors spread with no help from her agency and fans, she tried to reconnect with her fans, but suffers psychogenic aphonia, resulting in her losing her voice; this cause Miku to tension condemn humanity. Shido vows to keep his promise. Origami, Ratatoskr, terrorizes the territory to subdue Ellen. Westcott makes his appearance when Shido and Miku find Tohka. Shido is stabbed by Ellen with Tohka watching she goes berserk.

Tohka is born into a negative form with her counterpart sword Qliphoth and has no memory. Mana and Jessica reach the concluded battle. Jessica, dying in Mana's arms, tells how she always felt jealous and wanted to become strong for the DEM, Mana made her decision to dishonor Westcott. Westcott decides to retreat, although he briefly calls Shido "Takamiya". Tohka launches brutal attacks then Miku becomes vulnerable. Yoshino, Yoshinon, Kaguya, and Yuzuru regain their sanity. Shido took the hit to protect Miku. Tohka swings the sword of demise on the city, Shido flies towards her reminding her of him; dropping the Sandalphon, he seals her power once more with a kiss restoring her. Kurumi continue her search for the captive Spirit. The next day, Miku who is happy trusting Shido she purposely kisses him sealing her power much less her clothes. Miku invites everyone to listen to her latest concert then announces to her "darling" stunning the crowd and Shido. His competition among the girls' affection continues.