In Tokyo in the year 2020, Minato Sahashi has failed the college entrance exam twice, is awkward around women, and unemployed. Growing up, he could never stand up to his mother or little sister, a trend that continues to this day. In reality, Minato is extremely intelligent, yet his inability to cope under pressure results in his constant failure. As a result he has been branded an idiot and loser by many. One day, Minato meets a girl named Musubi, who literally falls from the sky. Minato soon learns that she is one of 'Sekirei' and he is her 'Ashikabi', human with special genes that allows them to "wing" (ie. form a contract with) Sekirei. This binds the Sekirei to him and allows them to use their full power in the elimination battle with other Sekirei. Made up of cute girls, buxom women, and bishōnen, the Sekirei fight in a dangerous and sometimes deadly competition (also known as "The Game" or "Sekirei plan") organized by Minaka Hiroto - chairman and founder of the mysterious and powerful MBI Corporation. Minato soon learns that being the partner of a beautiful girl is not all fun and games, especially when he discovers that an Ashikabi can have more than one Sekirei partner, and that's where the real trouble starts.
The story follows Nanami, a girl who finds herself homeless after her father leaves. She comes to the home of a boy who offers to let her stay over - only to discover it is a Shinto shrine. The boy happens to be a deity.