With the sudden appearance of the monsters that came to be called Dragons, the world had completely changed. Before long, within the human race supernatural girls with the power of the dragons, called "D," were born. The secret existence of the only male "D," the boy Mononobe Yuu, was forcefully thrown into the school where the girls of "D" gathered—Midgar, where he saw the naked body of one of the students, Iris. Furthermore, meeting his long-lost sister Mitsuki, Yuu seems to have been enrolled into this school...?! "When there's really no other choice, Iris, I will—kill you." "Can I really... believe you?" The curtains open as the "one and only story" about the boy who was supposed to become the strongest assassin and the incompetent girl unfolds—! Unlimited School Battle Action!
Yuu is sent to Midgar and encounters a naked girl at the beach. Iris is deluded into thinking that Yuu is an intruder, so she tries unsuccessfully to attack him, but then loses consciousness and is saved by him. While Yuu talks with Iris, his younger sister who he has not seen in two years, Mitsuki, appears and the two reunite. Afterwards, Yuu, who is enrolled at Midgar Academy and is placed into Class Brynhildr, meets with Haruka, who is the commander of the Midgar forces, and he tells her the reason why he was invited to Midgar, where is a Self-government educational institution whose aim is to collect "D" and to manage them and educate them. In the Brunhild classroom, Yuu shows his classmates the evidence that his is a "D", and they help him to realise that his ability is not a big deal. In the practice room, after Yuu and Iris limber up, Yuu receives a lecture on how to use the power of "D" by the girls. Haruka reveals to Yuu that the "D", who have an "armorial of Dragon", have the potential to transform themselves into a Basilisk, if a Basilisk falls in love with them at first sight. On the way home from school, Iris tells Yuu the reason why she fights, and talks about her childhood and growing up. She tells Yuu that she wants to become good friends with him, but suddenly the sounds of a siren reverberate, and then Iris's "armorial of Dragon" intensifies in response to a Basilisk.
Loki tells Yuu that it is his duty to prevent the girls at Midgar from becoming dragons and to kill them if they do. Iris has been having suicidal thoughts as she is dangerously close to becoming a dragon, but Yuu convinces her to think about living. The girls prepare for combat as Leviathan approaches the island.
While the girls are fighting Leviathan, NIFL soldiers attack Iris to stop her from becoming a dragon. Yuu protects Iris by defeating the soldiers using his dark matter guns. The girls penetrate the barrier with a coordinated attack and Yuu destroys Leviathan using the Babel cannon with Iris supplying dark matter to power up the attack.
Tear enrolls at Midgar Academy and claims Yuu as his wife as he was the person who saved her life when a fire burned down her home.
Tear's background is revealed as her family was killed when a dragon cult led by Kili burned her home and killed her parents. Tear takes pride in being a dragon because the cultists hold her in high regards, but Yuu convinces Tear to live as a human rather than a dragon. Kili arrives at Midgar to initiate an attack to take Tear away with her.
Kili attacks Midgar with the dragon Hecatoncheir that can regenerate. While Lisa looks after Tear, she is attacked and overpowered by Kili. Wanting to protect her friends, Tear agrees to go with Kili and become the Basilisk's wife. But Yuu convinces Tear not to go with her while he awakens the power of Leviathan to defeat Kili.
Kili retreats after being defeated by Yuu. Yuu devises a plan to defeat Hecatoncheir by drawing it out to sea where he could use Babel without causing any collateral damage to Midgar. Yuu uses an anti-gravity bullet to lift Hecantoncheir into the air and the girls generate a wind to blow it out to sea. The girls weaken Hecantoncheir's barrier and Yuu destroys it using Babel with Tear supplying the dark matter.
With Basilisk headed towards Midgar, Class Brynhildr heads to an uninhabited island to draw Basilisk away from Midgar knowing that it is after Tear. On the way to the island, Mitsuki and Lisa are at odds with each other over Miyako's death. Mitsuki explains her relationship with Miyako to Yuu. She was very close friends with Miyako, but she became a dragon when the Kraken invaded Midgar. Miyako ordered Mitsuki to kill her and Mitsuki reluctantly complied. With Yuu's help, Mitsuki and Lisa make amends with each other.
In the command room, Dylan gets the news from Loki that NIFL has finished preparing for the plan which is to make a critical attack on Basilisk. Yuu's party set out by ship to the place where they are to carry out their plan. After they arrive at the port, in one of the ship's rooms, Yuu tells Honoka that its was thanks to her that there was such a positive atmosphere on board the ship. Afterwards, Firill thanks Yuu for reparing Mitsuki and Lisa's relationship, then she gives a ticket to the hot spring to him as a thank-you. After Yuu enters the hot spring, several of his female classmates enter, and he realizes that he has been set up by Firill. Luckily, the girls get called away, saving Yuu from the problematic situation. The students of class Brunhild receive orders from Dylan not to interfere because NIFL is about to attack Basilisk. After Dylan orders bombing strikes against Basilisk by using the weapon formed in Mithril, this plan gets executed, but it comes to naught. Meanwhile, Tear's "armorial of Dragon" becomes hot in response to Basilisk and gleams with light.
After the Dylan's plan has gone awry, the execution of a new operation is entrusted to the Midgar. Having analyzed Basilisk's third eye, Haruka gives an overview of the new strategy to the students of class Brunhild, which is to form pairs and launch a strike on Basilisk, by infiltrating the volcanic island. She orders them to carry out the attack before the catastrophe beam can be fired. For this operation, the pairs consist of Yuu and Iris, Mitsuki and Ariella, Lisa and Ren, and Firill and Honoka. Yuu uses the dragon ability "anti-gravity", and he has a flashback to the time he was told by Charlotte that Mitsuki also has something akin to his power. Yuu notices Iris, who is in the midst of practicing hers skills, and asks her why she kissed him. In The medical room, the students of class Brunhild pledge to Tear that they will strive to achieve their mission, and subsequently they launch their attack on Basilisk. The students get into the designated positions beforehand and partner up, and then proceed to conduct attacks against Basilisk, using their magic which is enhanced by working in pairs. However, their magic is intercepted by the Basilisk's catastrophe beam. Tear's "armorial of Dragon" intensifies even further in response to it.
With the students in the catastrophe beam's line of fire, Honoka uses her power to get Yuu and Iris below the beam, while Yuu fires an anti-gravity bullet to direct the beam safely into the sky. The island is destroyed by Basilisk and students retreat back to the ship. After analyzing the attacks, Yuu determines that its third eye cannot fire the catastrophe beam in quick succession and its discharge time is five seconds. As such, Yuu comes up with a new strategy that involves dropping Mistilteinn, but with the students using dark matter to protect the Mistilteinn from the third eye's catastrophe beam for five seconds. Honoka shows her concerns about whether or not the plan will work, while Mitsuki decides that she will descend with the Mistilteinn, a plan Lisa expresses her disapproval of. However, Firill comes up with a better plan that makes Mitsuki the captain of the operation. That night, Tear is taken from the infirmary by Honoka, who Yuu figures out is actually Kili, and she intends to feed Tear to Basilisk to spare the other students.
Yuu defeats Kili in a fight to decide Tear's fate. As part of the agreement, Yuu's plan to destroy Basilisk goes forward and Yuu orders Kili to live on as a human. Kili kisses Yuu as she leaves asking him to show his superiority by defeating Basilisk. Mitsuki devises a strategy to defeat Basilisk with all possible fallback scenarios planned out. The students drop with the Mistileteinn and protect it from the first catastrophe beam discharge by Basilisk's third eye, but with the discharge having come much sooner than anticipated that the third eye had time to fire the catastrophe beam a second time, which destroys Mistileteinn. However, the blast creates an opening for the students to disable the third eye and immobilize Basilisk, allowing Yuu to destroy Basilisk using Babel. The students return to Midgar as Mitsuki's outlook on life has changed to a more optimistic one and Yuu tells Iris about his memory loss as a condition for using Babel, and Iris vows to stay with him.