Despite the numerous challenges he has overcome so far, Shidou Itsuka's mission with Ratatoskr is far from over. In a departure from his daily routine, Shidou encounters a starving woman lying on the street and ends up helping her. After the two arrive at her apartment, the woman introduces herself as Nia Honjou—a popular manga artist working under a pen name. However, cutting straight to the chase, Nia reveals that she is also a Spirit and is aware of Shidou's secret operation. Interested in seeing his charisma firsthand, Nia challenges Shidou to win her over on a date. As he strives for an opportunity to seal her powers, Shidou learns more about Nia and her history with Deus Ex Machina Industries, a name he is all too familiar with...

Shidou Itsuka carries on with his quest for Ratatoskr in finding Spirits and trying to seal their powers, all while maintaining his relationships with the ones he had already sealed. Moreover, as new Spirits appear, he must undergo more complicated trials—all to put a stop to further disasters as he discovers more about the Spirits' origin.

Thirty years ago, the Eurasian continent was devastated by a supermassive spatial quake—a phenomenon involving space vibrations of unknown origin—resulting in the deaths of over 150 million people. Since then, these quakes have been plaguing the world intermittently, albeit on a lighter scale. Shidou Itsuka is a seemingly average high school student who lives with his younger sister, Kotori. When an imminent spatial quake threatens the safety of Tengu City, he rushes to save her, only to be caught in the resulting eruption. He discovers a mysterious girl at its source, who is revealed to be a Spirit, an otherworldly entity whose appearance triggers a spatial quake. Soon after, he becomes embroiled in a skirmish between the girl and the Anti-Spirit Team, a ruthless strike force with the goal of annihilating Spirits. However, there is a third party that believes in saving the spirits: Ratatoskr, which surprisingly is commanded by Shidou's little sister! Kotori forcibly recruits Shidou after the clash, presenting to him an alternative method of dealing with the danger posed by the Spirits—make them fall in love with him. Now, the fate of the world rests on his dating prowess, as he seeks out Spirits in order to charm them.

A powerful necromancer known as the Corpse God dies during a legendary battle, only to be reborn as Polka Shinoyama, a young boy in modern-day Tokyo. In the process of trying to adapt to his new physical body, he gets targeted by various groups that deal with the supernatural. Among them is Misaki Sakimiya, a high school girl who can see spirits and is out for his blood from the very moment they meet. Attempting to make sense of this situation where unknown parties want him dead, Polka eventually meets Takumi Kuruya, a contractor skilled in surveillance and hacking, and Lisa Kuraki, a crime boss operating out of Shinjuku. Alongside these—and other unexpected—allies, Polka braves danger to reveal the truth of his reincarnation and the fate awaiting the world he now lives in.