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.

When Origami Tobiichi asks Shidou Itsuka out on a date, Shidou considers this his best opportunity to set the record straight and end their relationship. However, even with the help of the Ratatoskr crew, his attempts to break up with her fail; in fact, Origami gladly tolerates Shidou's humiliating requests and blunt comments! Shidou's unconventional mission incidentally complicates his relationship with Tooka Yatogami, and it seems that easing the tension is only possible by going on another date.

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.

One year ago, a UFO containing 150 aliens crash-landed off the shores of Kasai. Because no one could fix their ship, the Japanese Government decided to bestow upon them the designation DearS and make them into Japanese citizens, teaching them the language, customs, and culture of Japan. However, in order for them to become more familiar with human society, a home-stay program has been enacted to allow them to mingle with other humans. One misty morning, a truck carrying a capsule that housed one of these aliens ends up dropping it into the riverbank, releasing her from her confinement. She is eventually found by a high school student named Takeya Ikuhara, who saves her from being hit by a truck and takes pity on her, despite being extremely distrustful of their race and wanting nothing to do with them. Upon being named Ren, she imprints upon him as her Master and serves as his personal Slave, leaving him with a DearS who wants to remain with him no matter what and bringing his ordinary, alien-free days to an end.