Continuing where the first season left off, the sudden increase of Thanatos with the disappearance of the Aube Hunters has now left Arcadia in ruin. Desperation reigns high as the Religious Organization fights to battle the Thanatos. Six months had already past since Hidamari mansion burned to ashes, the Aube Hunters, once hailed as heroes, is now blamed for the appearance of Thanatos. Nevertheless, hope still exists for the reappearance of the Queen's Egg one day, who will become the savior of Arcadia. Unknown to many however, the Aube Hunters have actually been silently waiting for the awakening of Angelique, who has been asleep the entire time.

In search of true love, Kanako Miyamae transfers to Ame no Kisaki Catholic school, inspired by how her parents fell in love with each other there. There is just one difference, though: because men make Kanako break into hives, she has actually come to the all-girls school to find a partner of the same sex. When she meets the beautiful Mariya Shidou, Kanako believes she has found that special someone; however, there's more to Mariya than meets the eye—it turns out that Kanako's first love is actually a cross-dressing boy. Mariya threatens to expose Kanako's impure intentions unless she keeps his real gender a secret, and to make things worse, he also replaces her original roommate so that he can now keep a close eye on her. Maria†Holic follows Kanako as she looks for love in all the wrong places and searches for the girl of her dreams—that is, if she can survive being Mariya's roommate! [Written by MAL Rewrite]

Chiharu Kashima, captain of the Wizard Bureau's Crisis Countermeasures Division, is among a handful of people who can use magic. While frequenting his favorite bar, he is approached by a friendly man named Toyohi Utsumi. Having always dreamt of being a wizard, Toyohi is enthralled by the idea of meeting one. Much to the young Captain's surprise, Toyohi confesses that he has fallen in love with Kashima. While little time as passed, the two begin to spend more time together. Not all is well, however, as Kashima fears that magic is all that he has and Toyohi is only in love with Kashima the Wizard. [Written by MAL Rewrite]

Having failed 19 job interviews in one day, Juri Yukawa's dreams of moving out of her parents' home are utterly dashed. Stuck living with her working mother Nobuko, NEET brother Tsubasa, laid-off father Takafumi, and single-parent sister Sanae, the only hope for this family to raise a decent adult is her little nephew Makoto. However, this struggling family's life takes a turn for the worse when Makoto and Tsubasa are violently kidnapped by a mysterious organization and held for ransom. With only 30 minutes to deliver five million yen to the criminals, Juri's grandfather reveals a dangerously powerful secret to her and Takafumi. By offering blood to her grandfather's mystical stone, the three enter the world of "Stasis," a version of their world where time stops for everyone but the users. Having arrived at their destination, their rescue efforts go awry when they are assailed by a surprising group of people who are somehow able to move around within Stasis. While all hope seems lost, a monstrous giant known only as the Herald appears amidst the chaos, its intent and motivations as cryptic as the very nature of this timeless world. [Written by MAL Rewrite]