Nagisa is a hard-working girl who lacks a certain amount of faith in herself and desires to change herself. In addition to being a huge fan, she sees the opportunity to join AKB0048 as a way to reinvent herself. Despite her lack of faith, she cares deeply for her friends and will not hesitate to help them.
Four years ago, Nagisa, along with Yuka and Orine, were brought by Chieri to an abandoned mine where an AKB0048 concert was held. Yuuko notices the girls during the concert and waves to them and says goodbye before the ship takes off. After witnessing the concert and the battle between AKB0048 and the DES soldiers, in which AKB0048 won the battle, the four girls vowed to join AKB0048 one day.
On Lancastar, Nagisa attends a school alongside her friend Yuka. After a day of classes and meeting with Orine, Yuka shows the two of them an audition card she received from AKB0048, calling all girls who want to audition to send in a tape of themselves performing. Nagisa performs and doesn't think she got in, but is overjoyed when she, Yuka, and Orine are chosen to attend the auditions. At first Nagisa is excited, and runs home to ask her mother and father. Her father, who is a government official for DES, refuses to have his daughter involved in entertainment, and also orders her to remove her AKB0048 poster on her wall. Nagisa tearfully storms away, and her mother follows her up to her room, where Nagisa rails angrily against her father, while her mother watches helplessly. After a restless night, Nagisa decides to defy her father and run away to the auditions. As she leaves, her mother appears, and Nagisa thinks that she is here to stop her. However, she hands Nagisa a bow she made herself and wishes her luck in the auditions. After giving her mother a loving hug, she takes her bike and barely makes it to the space plane as it takes off.
In Episode 2, Nagisa and her friends are entering the station when an alert comes on regarding the disappearance of Chieri Sono, Zodiac's CEO's daughter. At that point, Chieri, in disguise, runs into Orine and knocks her over, and continues to run despite Yuka and Nagisa's scolding. Once on the ship, the girls meet three other auditioners on the ship, Makoto, Suzuko, and Sonata. Nagisa decides to search for Chieri, and finds her, while in her disguise, in a cargo bay. However, Chieri stuns her when she calls Nagisa her rival, and that Nagisa had better start thinking of the other girls as her rivals or else she will never make it into AKB0048 before vanishing.
As Nagisa has lunch with the girls and mulls over the meaning of Chieri's words, the DES attacks the ship, intent on capturing the six girls bound for the auditions. As Nagisa and her friends run, they are eventually cornered in a room with several other frightened passengers. When the DES break in, a soldier grabs Nagisa by her hair, but is quickly disabled when Takamina, Kojiharu, Tomochin and Sayaka burst into the room to rescue the girls and the passengers. As they make their escape, Nagisa realizes that her bow fell off in the scuffle with the soldiers and returns to get it. She is kidnapped by a soldier who grabs hold of her, but is saved when the soldier is shot by a now undisguised Chieri. Nagisa goes to thank her, but Chieri rebukes her for not being able to defend herself. As she does this, a DES bomb rocks the ship, and a chandelier falls and traps Chieri. Rather than run, Nagisa tries to help her, and soon Yuuko arrives and helps free Chieri. They then escape with the assistance and coverage by Mayuyu.
In Episode 3, Nagisa and her six friends join all the other girls who have come to audition for AKB0048. After being informed by Tsubasa that the requirement for passing the audition will be to have a successful performance of Beginner, Nagisa and the girls are escorted by Kojiharu off to practice. This includes battling robots, zero gravity environments, and firearms training. As Nagisa and the other auditioners collapse in the training room, Tsubasa informs them that the auditioners will not be performing Beginner, rather they will be defending AKB0048 during a performance of Beginner. The girls are shocked and expressed their tiredness as they get ready for bed. Chieri scolds them for their lack of commitment, and leaves to sleep elsewhere. Nagisa chases after her, with Yuka not far behind. The duo come across the current members of AKB0048 performing in the dance studio long after they other girls have gone to bed. When they start to fight, Nagisa bursts in and demands them to stop fighting. The members are stunned, then start to laugh as they find her misunderstanding amusing. As Takamina explains, these arguments lead to the girls learning from each other, and help them grow as a group. As Nagisa and Yuka go back to bed, they encounter two girls who want to tell Tsubasa to stop the training, and that it's unfair that the members of AKB0048 don't have to do the same. Nagisa begins to protest, but Yuka breaks in and scolds the girls just like the way Chieri scolded her.
After talking to the current members, Nagisa and her friends step up their game and excel in the training. As they descend to the guerilla planet, Nagisa is understandably nervous, but after a pep talk from AKB0048, her spirits lift a little. On the planet's surface, as AKB0048 begins their performance, most of the girls are eliminated right away. Nagisa, however, stands firm against the DES, and takes cover next to Chieri. When Chieri says that she will distract the DES mobile suit so Nagisa can get a clear shot of it, Nagisa chases after her, and as a result Chieri supposedly is shot. As Chieri lays on the ground with Nagisa beside her, Nagisa soon realizes it is paint. Then Tsubasa appears and informs the girls that they have passed the auditions and the whole thing was a ruse. Nagisa celebrates with her six friends as AKB0048 arrives.
As the girls arrive on AKB0048's home planet, Akibastar, Nagisa and her friends are treated to a performance of AKB0048 in their home stadium. Nagisa is wowed by the number of fans in the stadium, and that someday she will get to perform here. After the performance and meeting Kanata and Mimori, Nagisa is shown to her room by Mimori, where she fantasizes about becoming a "new me". She later joins Suzuko and Yuka in looking at the pictures of the past members who have held Center Position. The next day, at dance practice, when Chieri insults Kanata, she confronts Chieri in the locker room for her actions and words. Chieri explains her actions, then leaves. Later, Nagisa joins the other six girls in singing Shonichi down by the riverside to cheer up Kanata.
In Episode 5, Nagisa, after a rough start to the morning and an attempt to spend the day practicing, follows Chieri into the city. She follows her until Chieri notices and confronts her. After a misunderstanding with a passerby, she and Chieri share a few moments alone before Yuuko shows up, snapping a candid shot of the two. As Nagisa, Yuuko, and Chieri sit on the roadside looking at pictures of AKB0048 members past and present, Yuuko shares her memories of Atsuko Maeda, and that she admired her very much. After Yuuko leaves, Nagisa states she wants to succeed Yuuko, until Chieri reminds her that in order for Nagisa to succeed Yuuko, Yuuko must graduate. Nagisa changes her mind, and Chieri and Nagisa attempt to copy Yuuko's dance moves to which they somewhat succeed, earning applause from the passerbys. However, they vow to do even better, and to practice hard to catch up to Yuuko.
In Episode 12 and Episode 13, the understudies' debut performance is announced and set to take place on Lancastar. When Nagisa arrives on Lancastar, Mamoru and the other WOTA members inform her that her father has been imprisoned for refusing to call her back home, and she goes to rescue him. However, he refuses to be rescued by her, who he deems a terrorist, and Nagisa must leave to avoid capture. Following this, and seeing that the garden that her mother cared so much for, has fallen into disrepair. Nagisa then begins to lose her voice.
Later, during the concert, Mamoru convinces Nagisa's father to come with him and watch. While Chieri is trying to convince her to sing Nagisa no Cherry halfway through the song, Nagisa sees her parents and fans, and regains her voice. During this performance, Chieri's Kirara splits in two, one of which becomes Nagisa's.
Nagisa grows and becomes more mature and gains more self-confidence. Even though she was not elected, she is happy that Mimori and Chieri got elected as the members for the new single, even though sometimes she is jealous of Chieri in many ways.
After the General Elections, she and Chieri declare rivalry to become successors, and their Kirara shine very brightly. Yuuko said that the radiance is just like Acchan's.
In Episode 19, she is Mimori's stand-in because Mimori suddenly comes down with a succsetion fever. She realizes her 'goal' is different from Chieri and Yuuko, yet she still doesn't know who she wishes to succeed, though she has not given up on succeeding Yuuko, she does her best to try and discover herself. Chieri realizes Nagisa has changed. While performing as stand-in for Mimori and seeing Chieri and Yuuko out shine each other, Nagisa announces that she will also shine just as bright as the two and become Center Nova.
In Episode 21, there was an attack on Akibastar and Nagisa is seen fighting along with the other members.
In Episode 22, Nagisa is on the Flying Get and escaping the DES attack. Then she, along with Takamina, Mimori, Chieri, Kanata, goes to the prison cell where Mii-chan was held, and questions her about the attack and the Centre Novae disappearance. Later, when she was talking to Chieri at the staircase, she aims to become Centre Nova, open the door to the other world, and rescue Yuuko.
In Episode 26, the final episode, Acchan referred to Nagisa as the Atsuko Maeda that Yuuko wanted to sing with on stage. This was before Nagisa shined like the previous Acchan. After retaking Akibastar, Nagisa becomes the next Atsuko Maeda. Although Chieri is the new Center Nova, Nagisa claims that she will continue to try to surpass her to become Center Nova.