Fraîchement arrivée à Tokyo pour vivre avec sa tante, Misaki découvre sur un écran géant un combat opposant deux poupées, l'Angelic Layer. Icchan, un homme mystérieux qui la suit depuis son débarquement lui propose de l'aider à faire son propre personnage...

En allant à l'école Misaki fait la rencontre d'Hatoko, une toute jeune écolière passionnée par l'Angelic Layer, accompagnée par son frère et de l'amie d'enfance de ce-dernier qui s'avèrent être ses camarades de classe. Sur le chemin du retour, elle rencontre à nouveau Icchan qui l'emmène dans un centre d'entraînement où elle s'inscrit par erreur pour un combat...

Icchan procure à Misaki une carte lui permettant de participer aux tournois officiels et lui enseigne une technique pour l'aider à s'entraîner. Mais au moment où il la laisse seule, un autre joueur provoque la jeune fille en duel...

Misaki et ses amis participent au tournoi départemental de Tokyo. Alors qu'Hatoko gagne facilement son premier combat, Misaki a bien du mal a faire face à son premier adversaire qui utilise des attaques à base de glace à son avantage...

Misaki enjoys playing Angelic Layer and she loves Hikaru with all her heart, but when she goes up against the Power-type Vasquez, her confidence and self-esteem falters and has Hikaru engage in the 'hit and run' technique during battle, winning by a sheer stroke of luck. This angers Hatoko, who claims that Misaki has stopped believing in Hikaru and in herself.

Misaki has made it all the way to the National Games, but before the competition begins, there is one more thing she must do- find someone to act as her second during the upcoming fights. But when Misaki's friends come over to congratulate her on her success, it becomes clear that they all want they all want to be chosen as her second! And as Misaki attempts to sift through all the offers and select the one person she really wants as her partner, Shuko has a decision of her own to make, as to whether it is finally time for her to come and see Misaki.

With Hatoko by her side, Misaki heads for the opening ceremony of the National Games, determined to do her best no matter how stiff the competition. As the action gets underway, it becomes clear that all of the players are at the top of the game, but it soon becomes clear that there is one who still stands hand and shoulders above the rest- current champion ‘Shu' and her angel Athena.

The National Semis are here and it's Hikaru vs. Wizard, Oujiro's Angel. His Magic Guard seems impenitrable and Hikaru can't get a hit in edgewise. It's going to take all of Misaki's skill to get her Angel out of this one as Oujiro struggles with his own feelings about Misaki and his first love: her mother.

Misaki ponders the days when she was writing letters to her mother. But for now, it is time for the second semifinal as Sai, with her angel Shirahime, battles Shuko and her angel Athena.

The secret is finally out! Shuko has told Misaki that she is her mother. But now Ohjiro is going to have them meet face to face, and have Misaki learn the truth as to what her mother had been doing in Tokyo all these years.

Misaki and Hikaru are in the finals, and she is ready for biggest match ever as she faces three-time champion Athena, who is commanded by none other than her mother! Athena is the angel that Misaki modeled her own angel after, and with them having met each other for the first time in seven years, it is time for mother and daughter to communicate in the Layer. While only one angel will emerge as the champion, the battle is a win-win situation for everyone involved.