The stage is set. The preparations are complete. A grand battle royale known as "The Sekirei Project" is about to take the streets of Shintou Teito by storm. For this event, the shadowy corporation known as MBI has developed 108 "Sekirei"—advanced humanoid beings with extraordinary combat skills. Set free into the city, these Sekirei must search for their "Ashikabi," masters who can unlock and control their fighting potential through kissing. Once all the Sekirei are paired, they must battle until one team emerges victorious and claims the enigmatic grand prize.

Enter Minato Sahashi, a ronin whose life is as bleak as it gets. Weak-willed and unconfident by nature, his circumstances become even more hopeless when he fails his college entrance exams for the second time. However, when he encounters a Sekirei called Musubi, a bond sparks between them, and he finds himself becoming her Ashikabi. Although he begins to enjoy his life with Musubi and the other Sekirei he bonded with, he consequently finds himself increasingly embroiled in The Sekirei Project. If Minato wants to protect his newfound life, he will need to step up and participate in this demanding, high-stakes battle.