Misaki moves to Tokyo to live with her aunt. After getting lost at the train station she sees an Angelic Fight on a big screen. A mysterious man, Icchan, who followed her out of the train station tells her more about 'Angelic Layer' and helps her to create her own angel, Hikaru.

Misaki gets confused on her way to the first day of school when she meets Hatoko, a 5 year old girl who knows a lot about Angelic Layer, she also meets Hatoko's older brother, Kotarou and his best friend Tamayo. On her way home from school Misaki once again meets Icchan who helps her to make clothes for Hikaru and brings her to an Angelic Layer training center so she can practise movements on the Layer... However Misaki accidentally signs up for a match!

Icchan gets Misaki an Angel Card, a membership that will allpw her to enter official tournaments. He also teaches her a training technique, dancing with music, which will help her to learn the timing of fights. When Icchan has to leave Oujiro, Wizard's Deus, introduces himself and helps Misaki to practise. Later Misaki is tricked into fighting an unfair fight with another Deus.

After choosing her entry line Misaki and her friends attend the regional Championships. As she waits for her first battle Misaki watches Suzuka, Hitoko's Angel, fight her opponent, Nightingale, who she defeats with a single hit. Misaki's match doesn't go as well, her opponent's angel, Katrina', uses ice skates to gain speed and deliver a powerful, and nearly flawless, spin kick gains an early advantage.

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.