Louise tries to prevent Saito from looking at other girls, but her plan fails. The newly crowned Queen Henrietta assigns the code name 'Zero' to Louise for a mission. When they get home Louise insists she tell him about the misunderstanding that Agnes said. When he tried to explain she beat him until morning causing bruises all over his body. The next morning, Saito and Louise are informed that Henrietta has been kidnapped.

The supposedly dead Wales appears and takes Henrietta to Albion. He uses his vow from their earlier days to convince her into following him. Saito and Louise goes to rescue Henrietta. Wales, later revealed to be revived and controlled by Cromwell's ring, is defeated by Louise with a dispel spell. Wales is released from the control of the ring and asks Henrietta to make a new vow with him before dying again.

Julio Cesare transfers to Louise's school and shows an interest in her. He challenges Saito to a fight in which the winner gets to kiss Louise. Saito receives special training from Agnès but Louise shows up and attacks Saito in a jealous rage yet again. He fights against Julio the next day, but Julio loses on purpose.

Eléonore drags Louise, Saito, and Siesta back to the Vallière house, where Louise is announced to be engaged to a duke. Saito goes to talk to her at night but instead finds her sister who beats him like Louise does. Saito confesses his true feelings to Louise, makes out with her in a childhood boat, fights his way out of the Vallière residence, and heads back to school with Louise. She doesn't believe him about what happened in an earlier incident and beats him again while Siesta tells herself she is the only one for Saito.

Louise's sisters move in and make Saito do the work. Siesta makes a pass at Saito when Louise shows up. Just when Louise was about to strike him with a newer whip an explosion happens. A thief stole something from the principal's office and the principal marked the woman with a magic seal on her chest. Saito tries to do it secretly but Louise finds him and tries to hurt him again. Then a commotion in her eldest sister room gets their attention. The thief is found out and when everything is done and over with because Saito didn't tell her what he was ordered to do along with other things that was justifiable she beats him with her new whip out of spite.

Saito and Louise are ordered to be at Scarron's inn to receive further instructions. They take their previous positions and costumes back, and are surprised by Gulio's appearance. Saito runs into Henrietta who asks him to protect her as she poses as a commoner in order to lure out one of her enemies. Saito and Henrietta evade detection from the soldiers searching for the Queen by behaving like sweethearts, while Louise learns of the details of the Queen's mission from Agnes. In a theater in town, while Scarron and his girls are in the middle of performing a play, Henrietta confronts her enemy.

Henrietta is convinced to sign a declaration of war against Albion. News of a victorious battle for the Tristain and Germania allied forces reaches a town that Louise and Saito are currently in. Saito discovers a sailor uniform on sale at a clothes merchants shop, and buys it, opting to give it to Siesta rather than to Louise. Upon returning to the academy, the two join Agnes and Julio on exploring a secret archive hidden beneath the school, which Agnes was denied permission. Agnes wishes to obtain the information there regarding her home town of D'Angleterre's burning to help carry out her revenge against those involved. Eleonore is picked to open to lock to the entrance. As the group heads farther down, they are joined by Siesta, who is wearing the sailor uniform Saito gave her earlier. After discovering that Saito gave the sailor uniform to Siesta because Louise lacked the chest size to make it look good, Louise blows a part of the cave in the way they came. With little to do but move further, the group finds the archives and are sent to look for the records regarding the town of D'Angleterre's burning 20 years ago. When Siesta trips and makes a mess of the books, Eléonore returns them to their proper place with magic, which triggers the archives' security system and begins to bring the bookshelves to a close. Agnes finally finds the information regarding D'Angleterre's burning, but a part of the page that lists the person who led the attack is missing. The group narrowly escapes the collapsing of the bridge that led them to the archives. Upon realizing that Louise had blocked their way out from before, Julio grants Saito permission to have intimate moments with Siesta. Siesta is happy to oblige and Saito also thinks it to be a good idea, however, Louise is watching and is preparing to blow something else up. When Saito points out that the cave in she made earlier is in the opposite direction, Louise tells him to shut up and blows them up anyway.

Albion sends hired mercenaries to make a surprise attack on the Magic Academy and take all of the people from the royal families hostage. Saito and his friends plan on how they will rescue the people taken hostage as it will take too long for the reinforcements to come from the palace. It is discovered the captain was one of those who attacked Agnes's town D'Angleterre's and burnt it to the ground 20 years ago.

Colbert sensei and Saito devise a plan to enter into the building and save the hostages. Benubiro explains to Anies how his captain Snake of the Flame ruthlessly burnt the women and children to ashes. The team use their combined magic to enter the building. During the attack, Benubiro recognises Colbert-sensei who is in fact his captain Enja, Serpent of the Flame. The two enemies begin a heated battle. Agnes becomes furious and charges towards Colbert sensei. Benubiro fires a lethal fireball towards Agnes to stop her from interrupting them, Colbert-sensei pushes her away from the blast and is struck in the crossfire. Agnes takes her revenge for her town upon Benubiro and defeats him. Colbert-sensei in his last moments explains what had occurred on that fateful day. He had been given orders to destroy D'Angleterre's Town as it had been reported to be struck with a deadly plague. After discovering there was no plague, he discovers a girl (Agnes) the only survivor and he carries her to safety. Agnes is still infuriated and she holds up her sword to strike a final blow to Colbert-sensei, but he dies before she can do so. Louise and Saito are saddened by the death of their teacher, whereas Agnes is still undecided if she will ever forgive him.

Henrietta has a special mission lined up and Louise and Saito are the perfect candidates. But Saito hesitates to go into battle because of what Mr. Colbert mentioned before.

Henrietta's forces enter South Gotha and claim it. Scarron's traveling tavern sets up shop, and Saito and Louise are reunited with Siesta, Jessica, and Guiche. Guiche shows off a medal and relates a story of coming back from the dead, which no one believes. Using the Ring of Andavari, Sheffield causes some of Henrietta's troops to attack the city from within.

Louise is secretly approached by one of Henrietta's advisors and is asked to hold the enemy off while the Queen escapes. Knowing that it is a suicide mission, Louise plans to send Saito to safety, but not before marrying him. Catching wind of her plan, Saito uses a sleeping potion on Louise after they wed and asks Julio to take care of her and sets out to meet Albion's advancing troops. Louise faints before she can tell him she has always and still loves him. Despite his valiant efforts, Saito falls in the battlefield. Back at the academy, Louise collapses in grief at Saito's death, however, suddenly the magical flower that is connected to Saito unexpectedly comes back to life. Louise runs out and meets Saito who is very alive. When Saito fell, the Fairy, who resembles an Elf, saved him, revived him from death and healed him back health. While explaining, Saito mentions the fairy's large breasts which then Louise uses as an excuse, flies into a jealous rage, forgets about being sad about him and starts trying to explode Saito yet again.