CPU Candidate Nepgear accompanies Neptune and the other CPUs to the Gamindustri Graveyard to fight CFW Magic. However, Nepgear watches helplessly as each of the CPUs, including her own sister are unable to beat her. She then finds herself captured alongside them as Magic turns her sights on her.
Three years later, Nepgear is rescued by Compa and IF who are there to save her and the CPUs. CFW Judge, who has been tasked with guarding the captured goddesses, fights against them. Proving to be no match for Judge's power, Nepgear uses the small bit of sharicite brought by Compa and IF to blind him so that they can escape. She passes out shortly after.
Nepgear awakens in the Planeptune Basilicom and is greeted by Histoire, Compa, and IF who give her the basic rundown of Gamindustri's condition. Nepgear is tasked with gaining the aid of the other CPU Candidates and the mascot characters of each nation. While Histoire searches for the Planeptune mascot, Nepgear is taken out for rehabilitation by IF and Compa. It is then that they learn Nepgear is unable to transform due to being afraid.
When Histoire locates the mascot, the girls head to the Virtua Forest Depths where they find Underling trying to destroy the Planeptune mascot. Underling proves to be too strong for Compa and IF and manages to deal with them easily. Just as she is about to go for Nepgear next, IF jumps in the way to defend her and then kisses her to shock her into HDD. Now transformed, Nepgear manages to defeat Underling. Nepgear offers Underling the chance to escape but Underling does exactly as she planned and destroys the Planeptune mascot before fleeing.
Luckily for them, the Planeptune mascot had transferred some of her powers elsewhere before being destroyed, and gives that power to Nepgear in the form of a Purple Disc. Nepgear reports back to Histoire to tell her of their success before they head off to Lastation.
During Nepgear's time in Lastaton, they make efforts to locate the Lastation mascot and to obtain Uni's help in saving the CPUs. When she first meets Uni, they hit it off very well, but upon Uni learning that Nepgear is the CPU Candidate of Planeptune, she becomes highly upset and refuses to cooperate with her. In the middle of them searching for the hematite to give to Kei, Nepgear is forced to fight Uni who will not give them what they want unless Nepgear wins. Once they manage to finish up all their work in Lastation and obtain the help of the mascot character, Nepgear asks one last time if Uni would like to join them. Uni says she'll think about it, which makes Nepgear happy.
Histoire informs of ASIC attacking a nearby island in Planeptune territory and requets for Nepgear and the others to lend them their aid. They meet Falcom for the second time who is defending the island from the ASIC threat and is happy to receive their help. Nepgear and her companions easily deal with Underling's scheme and tell Falcom that the island is now safe.They return to Planeptune to inform Histoire of their success of obtaining the mascot characters and IF soon becomes notified of Lowee losing 90% of it's shares.
Nepgear helps Lowee in their time of crisis, and saves the twins who get wrapped up in CFW Trick's plot. Mina expresses her gratitude and allows Rom and Ram to travel with Nepgear to save their sisters. As they make their way from Lowee, they receive word from Kei that Uni has gone missing and immediately head for Lastation next to find her.
They learn that Uni agreed to fight with a large inhumane figure at Midcompany and hadn't returned since. The party heads to the location and sees Uni unconscious on the ground. When she awakens, she explains that she had been defeated by CFW Brave who is one of ASICs leaders. They take her back to town only for her to go missing for a second time. Nepgear finds Uni the Endless Zone dungeon and ends up facing off against CFW Brave alongside her. Together, the two of them manage to fight him off. Feeling more confident in herself, Uni finally asks to join the party so she too can help save the CPUs.
With the other CPU Candidates and the mascot characters in tow, Nepgear and her companions head to the Gamindustri Graveyard to rescue the CPUs. When they arrive, she heads to the place where they saw the CPUs last and encounter CFW Judge for a second time.
Nepgear is unsure of her abilities to defeat Judge, due to being helpless against him the the first time they fought. Thanks to the encouragement from her friends, Nepgear awakens a hidden power locked inside of her and gains the Lilac mk2 processor unit set. Together, Nepgear and her party takes down CFW Judge and manage to save the CPUs using a strengthened Sharicite. Relieved to have finally rescued her older sister, Nepgear breaks down into tears and gives her big hug.