Thirty years ago a strange phenomenon called a "spacequake" devastated the center of Eurasia, claiming the lives of at least 150 million people. Since then, smaller spacequakes plague the world on an irregular basis. Shido Itsuka, a seemingly ordinary high schooler comes across a mysterious girl at the ground zero of a spacequake and learns from his sister Kotori she is one of the "Spirits" who are the real cause of the spacequakes that occur when they manifest themselves in the world. He also learns that Kotori is the commander of the airship Fraxinus, crewed by the organization Ratatoskr, and is recruited to make use of his mysterious ability to seal the Spirits' powers thus stopping them from being a threat to mankind. However, there is a catch: to seal a Spirit's power, he must make her fall in love with him and kiss him.
Beginning with the original spacequake 30 years ago, the ditzy Kotori and her brother Shido are introduced as modern day residents of Japan. For the opening ceremony, Kotori and Shido make a promise to meet at a diner later that day. As school ends for Shido, a spacequake alarm sounds throughout the city for the citizens to enter shelter areas immediately. After being unable to contact his sister, Shido uses her GPS to confirm that she is still within the city according to their promise. He leaves the shelter to find her and in doing so, is outside when the spacequake occurs thus meeting his first Spirit. After the battle between the Spirit and the AST, where Shido learns that Origami is a part of the AST, Shido finds himself among the group Ratatoskr on the airship Fraxinus learning about the Spirits, his sister and the organization she is a part of.
Shido is undergoing stage two of his training which is practical application upon real humans. First is his teacher who, with the assistance of Reine and Kotori, falls head over heels in obsessive love with him. Running away from her, he bumps into Origami. He uses her for practice but ends up unintentionally starting a relationship with her. A spacequake alarm occurs and the Princess Spirit is expected to appear at Raizen High School. With the students evacuated, Shido heads inside the demolished section of the school to confront the Princess. Shido makes a connection with the Princess and names her Tohka. The AST shows up and engages Tohka from long range with their rifles to drive Tohka out but Origami sees Tohka with Shido and assumes that Tohka is holding him hostage. Since Shido is now her boyfriend, enraged, Origami flies to engage Tohka in close combat. Tohka is lost during an explosion and Origami is taken away for minor hospitalization. The next day, Tohka appears before Shido as he is rummaging through the rubble so that they may go on their date.
Shido and Tohka are on their date being overseen and supported by the Fraxinus crew. Tohka mistakingly assumes that each variety of food she is consuming at first is a "date". Not accustomed to a crowd, when the couple enter the shopping area she assumes that humanity is launching an all out attack on her. Origami observes them from the shadows while Shido and Tohka go from a high priced restaurant to south of the station where they enter an improvised shopping area. Tohka is able to indulge in the foods present to her desire but notices that Shido doesn't seem to be having fun. They move on to an arcade that is dominated by crane games which Tohka mistakingly assumes is the "mecha team's" secret base. In the course of playing for a prize that has caught Tohka's eye, Tohka inadvertantly voices her bond with Shido. They make their way to a cliff edge where Tohka finally finds out what a "date" is and sees why the "mecha people" want to kill her as she keeps destroying a world that's so kind, fun and beautiful. Meanwhile, Origami is given permission to fire but as she fires, Shido pushes Tohka out of the way and is killed instead. Enraged by Shido's death, Tohka rampages on a stunned Origami as she sees the AST as people who only want to kill and die. Before Tohka can swing the killing blow on Origami, Shido is revived with his wounds completely healed and falls from the sky towards Tohka. To prevent the city from being destroyed by a critical state Halvanhelev, Tohka kisses Shido while they glide down to the cliffedge as Tohka's Astral Dress disappears. Her last request is that Shido take her on a date again.
Shido meets Yoshino for the first time while running through a shrine on a rainy, ill-forecasted day. Believing her to be just a girl, he goes on about his way. At school, Tohka has made cookies and competes with Origami for Shido's attention. Arriving home, Shido learns that Tohka will be living in his house since he has sealed her powers. Kotori explains that it is also training as Shido still has to assist in sealing more spirits. Later, as a spacequake alarm goes off during school, Shido heads out to find it is Yoshino that is the cause. Tohka is left in the shelter while Shido goes out to meet Yoshino only to have Tohka follow him and witness the two accidentally having kissed. Tohka retrieves her powers from Shido but only to provoke Yoshino who attacks while leaving. Utilizing her angel Zadkiel, Yoshino is also able to escape from the AST nearby while Origami eyes Yoshinon, Yoshino's puppet.
Tohka is avoiding Shido due to her feelings about what happened between him and Yoshino. She talks with Reine and receives advice and clarity about what occurred. During this time, Shido helps Yoshino look for her puppet, Yoshinon. Yoshino gets hungry while searching so the two go to Shido's house to eat. It's revealed that Yoshinon is Yoshino's friend because he is strong, cool, bold, and is essentially a hero that is everything Yoshino wants to be. As Shido is getting close to Yoshino, Tohka barges is spouting an apology but misinterprets the situation. Yoshino teleports away, Tohka barges out again, but Shido learns that Yoshinon is at Origami's place. Origami forcibly makes progress between them when Shido comes over but as the conversation turns to Spirits, she gets notice of a mission. Yoshino is being targeted by the AST but Shido plans to save her with Tohka's help. As Tohka acts as a decoy, Shido makes it through Yoshino's barrier with Yoshinon to fulfill his promise. With her trust in him established, Shido seals Yoshino's powers. In the last few scenes, it is revealed that the housing for the Spirits has been completed so that Tohka and Yoshino may move in.
Tohka and Yoshino desire to visit a hot springs so Shido makes the arrangements with Kotori for them to go to Tenguu Gokuraku Hot Springs. Kyouhei attempts to convince Kotori to go but it's revealed that he has ulterior motives. His punishment is to dig a hole and refil it for the next week. Meanwhile, Kusakabe is informed that the DEM Corporation is going to send reinforcements. Kusakabe also finds out that due to the increase in the Spirit's attacks the alert level has been raised causing the group's vacation trip to be cancelled. Convinced by an AST member, Kusakabe decides that the AST will instead go to the hot springs. Origami receives a phone call from Shido where she overhears that he'll be going to the Tenguu Gokuraku Hot Springs with Tohka. While riding, Yoshino is given affectionate attention by Shido which frustrates Tohka causing her to collapse the road. This in turn disrupts the train the AST is riding on underground. The AST arrive at the surface behind Reine, Shido, Yoshino and Tohka. To prevent contact of the two groups, Ratatoskr intervenes in the path of the AST with multiple obstructions. Shido invites Kotori after seeing her but is interrupted while Kotori is informed of the situation regarding the AST. Kotori orders Date Town to enter Battle Mode Level 2 with authorization to open fire on the AST leading to a battle in which stray ordinance causes [Yoshinon] to fly off. Shido goes to find [Yoshinon] in the midst of the firefight and is almost killed by Ratatoskr's Destruct Mode. Tohka saves Shido from the attack while being overseen by Origami and fellow AST members. Everyone reaches the hot springs but due to Yoshino's actions, it has partially frozen. Kannazuki finds a hot springs that Kotori, Shido, Tohka and Yoshino end up enjoying by themselves. Mana Takamiya is then shown as arriving in Japan.
Mana is having a 10v1 practice match against Origami's unit before having introduced herself at the briefing AST's previous battle with Hermit where she unknowingly reveal's herself to be Shido's sister. Kurumi transfers into Shido's class revealing herself to be a Spirit to get closer with Shido. During her time touring the school with Shido they're followed by Origami and Tohka, but as Shido is attempting to seduce Kurumi she is also attempting to do the same to Shido. After school, Kurumi kills three humans and is confronted by Mana. Mana then runs into Shido later on that day. Taking her to his house, what Mana shares about herself leads to a quarrel between her and Kotori but ultimately leaves everyone with more questions than answers. During school the next day, Shido finds out that Kurumi was killed during her confrontation with Mana yet she appeared at school. Origami questions Kurumi in a secluded place and finds out that Kurumi is ultimately after Shido.
Shido invites Kurumi out but is forced on a polygamous date when Tohka seduces him and Origami forces her plans upon him for a date. Shido is unable to deny any of them as Tohka would be heartbroken, Origami would be suspicious and his plans to seal Kurumi depend on the date. With their dates occurring around the same time and their entertainment venues located rather close to each other, Ratatoskr assists Shido by teleporting him to each girl's location while monitoring their emotional levels. After Shido leaves Kurumi, she finds some boys shooting at a stray cat and convinces them to let her play with them. Ratatoskr loses sight of Kurumi as Origami and Tohka run into each other. After they both proclaim their trying to find Shido for their date, Origami runs off concerned there may be another. Shido returns to look for Kurumi but finds blood, body parts, and Kurumi killing a man. As she holds Shido within her clutches, Mana intervenes wearing her CR Unit.
Mana kills Kurumi and explains everything to Shido. After he is forced away, he avoids Origami and Tohka after running into them because of seeing the death Kurumi caused. Tohka finds out the reason for Shido's behavior and continues her date with him to try to cheer him up. After gaining some insight to Kurumi, the next day Shido declares to Kurumi that he'll save her. Kurumi goes to the school rooftop while encasing the school in her field to dissuade Shido from trying to save her. Mana is confronting Kotori about Ratatoskr and attempting to use it as leverage against Kotori so she'll release Shido from the potential danger he's in. While Kurumi is threatening the school and the town, Origami and Tohka are engaging in battles with other copies of Kurumi. Shido convinces Kurumi only for her to be killed by another Kurumi. As Tohka and Origami show up, it's revealed that the hands in Kurumi's shadow are actually the hands of other copies of herself. Kurumi takes everyone hostage and attempts to blow a spacequake only for it to be blown away. Kotori appears explaining the cancelling of the spacequake while in her Spirit form. She has taken back her Spirit powers from Shido temporarily to fight Kurumi.
Kurumi and Kotori start fighting after a short conversation. Kurumi used one of her skills to make Kotori stay still, create copies of her, and shoot her a few times. Kotori fell over after Kurumi's last shot but Kotori's healing skill enables her to not die. Then, the shocked Kurumi send her copies to kill Shido but he was pushed away by Kotori and the copies were killed. In the heat of the fight, Kurumi used her one of her skills to Kotori but it only worked for a while. Kotori used her weapon to shoot Kurumi's angel after the frightened Kurumi summoned her copies to shield her. He immediately stands in front of Kurumi to shield her, knowing Kotori is no longer herself at that time when he tries to reason with Kotori to not kill Kurumi. Later, after the shot have launched, Kotori suddenly regained conscious and deflects the shot. Shido woke up on the bed after having a dream of the event that happened 5 years ago. He went to meet Kotori for information of her powers after being calmed down by Reine. He left the place in despair to meet Mana and Origami in the hospital after he heard from Reine about Kotori's condition. Being unable to meet Mana, Shido instead meets Origami, who tries to get him closer to herself. Before Shido exit Origami's room in the late evening on that day itself, she told him of her intend to kill the Spirit of Fire after finding it for 5 years to avenge her parent's death, and the reason that she joined AST.
Shido is contemplating the situation regarding Kotori involving the events five years prior including the statements made by her and Origami about the apartment fire. While he meets with Reine to discuss the details regarding the date with Kotori, Origami is informed about high-tech gear coming into the base in two days by Ryouko while she visits Origami in the hospital. Ratatoskr's headquarter's personnel have all agreed that going to Ocean Park with Kotori is the ideal venue for Shido's date so Shido undergoes a training session outlined by Reine to prepare involving Shido taking Tohka and Yoshino to buy swimsuits. As Tohka asks about a swimsuit, Origami appears and teases her about it being a new piece of anti-Spirit equipment but reveals that her true motive for joining them is to inquire of Tohka about the Spirit of Flames to the point of politely being courteous in her questioning. Finding Tohka's information useless, Origami pressures Shido into giving his opinions on her choice of swimsuit. Tohka and Origami turn it into a battle in that whoever turns on Shido more gets to go on a date with him. Yoshino ultimately wins but back on Fraxinus, Shido watches the video of the fire from five years ago. Recognizing ordinary video noise as an actual person initiates a series of flashbacks that lead to Shido blacking out. During Kotori's date the next day, Tohka and Yoshino tag along to help Kotori ease up and be able to partake of the actual events. As Shido sees Kotori resorting to pharmaceuticals to counteract her deteriorating mental condition, his determination is invigorated so he goes about the date with just him and Kotori. At the AST base, Origami gets a firsthand view of the DW-029 Annihilator Gear codenamed “White Licorice” sent there by DEM Industries for use by Mana. In talking with Ryouko, she's indirectly told that they have footage of the battle between Kotori and Kurumi. In the last scene, Origami is staring at a frame from the footage showing Kotori as she realizes who Efreet is.
Picking up directly from Origami seeing Kotori, a frightened Kotori is with Shido at the amusement park riding various roller coasters and attractions on their date. Without communications, Ratatoskr can only monitor with Kyouhei making masochistic comments to the opportunities Shido should have taken. While separated, Yoshino tells Tohka what she overheard about Kotori being a Spirit and how Shido is trying to seal her powers. Origami steals the DW-029 Annihilator Gear codenamed “White Licorice” and suddenly attacks Kotori as she is talking to Shido. Origami enters into a rampage, going into a full offensive when she witnesses Kotori change into her Spirit form. Before Kotori strikes a finishing blow, Origami tells her of how she killed Origami's parents five years ago sending Kotori into a state of temporary shock. Shido intervenes, delaying Origami but as she is about to fire Tohka and Yoshino arrive. Tohka strives to stop Origami but as her ordinance is exploding ever closer to Shido and Kotori, the latter two kiss effectively sealing Efreet. During the kiss, Shido and Kotori remember exactly what happened five years prior. Shido pleads with Origami as she reaches the operational limit of White Licorice and collapses from exhaustion. Kurumi is seen on a rooftop only commenting "This is not enough." Back on Fraxinus, Reine reveals that the date wasn't necessary as Kotori's affection levels hadn't wavered since Shido first woke. Kotori returns to fill out reports asking if what Shido said was true. Kotori gets uncharacteristically embarrassed as he confirms his love of her, but as Shido finishes saying simply as his sister he receives swift punishment. During the credits it's shown that White Licorice has been returned and Origami has been hospitalized. As Shido is going to kiss Tohka he's interrupted by Ratatoskr and finally [Yoshinon] along with Yoshino who simply say "To be continued. Sometime."