Mahiro Yasaka, a typical high school student, faces a grave danger when a vicious monster attacks him. Just when he's about to give up, a silver-haired girl, Nyaruko, comes to his rescue. She claims to be Nyarlathotep, a deity from HP Lovecraft's Cthulhu Mythos, who has the power to alter her form. Nyaruko explains that she's been sent to Earth by the Space Defense Agency to safeguard it. Nightgaunt, the malevolent being that was chasing Mahiro, intended to abduct and sell him as a slave. Nyaruko, along with her friends Cthuko and Hasuta, assist Mahiro in avoiding several extraterrestrial dangers that threaten Earth's well-being. However, as the three eccentric aliens grow close to Mahiro, Nyaruko falls head over heels in love with him, and imposes herself on his household. Her infatuation makes Mahiro's life miserable, and the trio becomes a constant source of annoyance with their outrageous antics.