"Rokujouma no Shinryakusha!?" centers on Koutarou Satomi, a high school student who rents a cheap apartment, Room 106 of Corona Apartments, to alleviate his financial struggles. However, the room becomes the focal point of a series of bizarre and comedic conflicts as multiple factions lay claim to it. These factions include a ghostly girl named Sanae Higashihongan, who haunts the room; a magical girl, Yurika Nijino, sent to protect Earth; an underground dweller, Theiamillis Gre Fortorthe, seeking refuge; and an alien princess, Kiriha Kurano, aiming to conquer Earth. Each group believes they have a rightful claim to the room, leading to chaotic and often humorous confrontations.

As the story progresses, Koutarou finds himself at the center of these disputes, inadvertently forming bonds with each of the girls. The narrative shifts from episodic conflicts to a more cohesive plot as the characters uncover the room’s deeper mysteries. It is revealed that Room 106 holds a connection to the ancient civilization of Forthorthe, which ties into the origins of the magical and extraterrestrial elements in the story. The group eventually bands together to face larger threats, including a powerful enemy from Forthorthe’s past, Lord Vandarion, who seeks to exploit the room’s hidden powers.

The series balances comedy, romance, and action, with each character bringing unique dynamics to the group. Koutarou’s resourcefulness and growing leadership skills help unite the diverse cast, while the girls’ individual arcs explore their motivations and personal growth. The story delves into themes of friendship, loyalty, and the importance of understanding others, as the characters learn to coexist despite their initial conflicts. By the end, the once-disparate group becomes a tightly-knit team, ready to face future challenges together.