Minato Sahashi, a typical ronin student, finds his life suddenly changed after meeting a strange girl named Musubi. Minato discovers learns that she is a 'Sekirei' and that he is her 'Ashikabi' (ie. Master).

Minato takes a job at a local construction site where he meets another Ashikabi, Seo Kaoru. With Seo's help, Minato infiltrates a nearby botanical garden, drawn by visions of a young Sekirei girl named Kusano, after Seo and his Sekireis eliminate a MBI roadblock in front of the garden. Musubi soon arrives and with her help, Minato rescues Kusano, who later makes Minato her Ashikabi.

The mysterious girl turns out to be Matsu, a Sekirei who has been hiding at the Inn. Matsu becomes Minato's third Sekirei. Minato has dreams of another Sekirei, later identified as Tsukiumi, a Sekirei that despises Ashikabi. Minato and Kusano go looking for her and encounter Seo. Hikari and Hibiki soon arrive chased by Tsukiumi.

Sekirei #95, Kuno, and her Ashikabi Haruka attempt to escape Tokyo despite a lockdown, but are pursued by MBI soldiers and members of the Disciplinary Squad. While Uzume visits her Ashikabi, Chiho, in the hospital, Yukari resolves to help Shiina search for Kusano. Matsu uncovers information about Sekirei being defeated by an unidentified assailant. Tsukiumi and Musubi confront the 'veiled' Sekirei who has corned Kuno and her Ashikabi, unaware that it is Uzume.

Minato is in despair as Musubi is down for the count, but refuses to give up, much to Benitsubasa's irritation, who proceeds to deal with him. Battles rage elsewhere as Kuno and Shiina (along with their respective Ashikabi) come under assault from various adversaries, and thus decided to have themselves winged, repulsing the attacks. But in a twist of fate, someone from Karasuba's past comes to Minato's aid in assisting Kuno and Shiina.

Seo aids Matsu in securing MBI data for Higa while Minato and Musubi confront Minaka before he escapes, leaving the MBI Tower as it gets destroyed. Karasuba engages Musubi after she threatens death of Minato's other Sekireis. Under a Norito, Musubi was able to defeat Karasuba for the latter to concede defeat. With the tower destroyed, everyone began to return back to their normal lives. Higa was covertly given false data after Seo advised Matsu. Thanks to the data recovery, Chiho was successfully cured of her sickness.