Three years ago, the long war between the Royal Empire and the Republic of Frost came to an end. With both nations a long way from recovery, a passionate young woman named Alice L. Malvin leads the Pumpkin Scissors, a unit of the imperial army specializing in war relief. During a mission to assist a village occupied by renegade soldiers, Alice meets Randal Oland, a scarred former soldier with a sordid past and kind heart. Encouraged by the efforts of the Pumpkin Scissors, he joins the team on their mission. During the assault, however, Randal enters a trance-like state prompted by a mysterious blue lantern. As a result, he acquires monstrous strength and decimates the enemy forces. Despite having witnessed Randal's disturbing transformation, Alice invites him to join her squandrant, confident that his gentle nature will prevail and make him a perfect fit for the Pumpkin Scissors.

Two weeks have passed since the dilemma between Maiku, Karen and Miina was resolved, but their lives are more hectic than ever. Karen has become possessed in her newly discovered brother and Miina is desperate for attention as well, which leaves little time for Maiku to concentrate on his work. Therefore he decides to head out in the woods and set up a camp, where he can be work in peace. But, as always, we have Morino who is up to no good. To make things a bit more interesting, she organizes a field trip to Maiku's camp site, and encourages everyone to make some good summer memories.

Saku Ooyagi returns to his hometown after seven years and is soon reacquainted with his childhood friend, Mihoshi Akeno. The reunion is far from merry since the last memory they have of each other is of her falling off a tree and him saving her. In any case, Mihoshi is determined to improve their relationship and forces Saku to join the astronomy club she founded.

Little time has passed since the Magic Knights’ final confrontation with Princess Emeraude’s Mashin. Still haunted by the princess’ death, Hikaru Shidou returns to Tokyo Tower. There, she meets her friends Umi Ryuuzaki and Fuu Hououji for the first time since their spontaneous quest to save Cephiro. Plagued by nightmares of the realm she had left behind, Hikaru is relieved to find that her companions too want to return and serve the kingdom they once so dutifully protected. The Magic Knights’ wish is answered, for at the top of Tokyo Tower, the three are blinded by the same great light they had seen on the day they first met. Once more on the back of a flying fish, the group returns to Cephiro—a world now desolate and in ruins. With the collapse of the Pillar's power, monsters freely roam the land while three nations seek to annex Cephiro with hopes of seizing the Pillar for themselves. Complicating things further is the mysterious Lady Debonair, who proclaims herself to be the rightful heir of the fallen country. Now confronting graver stakes and radically different enemies, the three Magic Knights set forth once more to save Cephiro and bring peace. With the bonds they have forged together, the trio stands united in the face of such a great challenge.