Hyperdimension Neptunia Victory features a total of 11 chapters, 2 which can only be seen through special requirements.
Neptune faces off against Noire, Vert, and Blanc in a game and is defeated due to them teaming up against her. Nepgear arrives with refreshments for them and Histoire comes shortly after to scold both of them; Neptune for lazing around and not properly acting as CPU, and Nepgear for enabling Neptune's behavior. The other CPUs leave and head back to their own nations, leaving the two deal with Histoire on their own. Neptune and Nepgear are kicked out of the Basilicom until they do some work. With that, the two head to The Guild, to complete some quests. In the middle of this they also travel to the other nations to visit the CPUs and the CPU Candidates.
They also end up meeting Rei Ryghts who is running a movement against the goddesses. She flees not to long after seeing them. They return to the Basilicom and meet Compa and IF and learn more about the movement against CPUs but IF says that Rei seems harmless to say the least. Rei, who had gotten lost after running, ends up meeting Croire and getting a dark energy forced into her mouth.
The next day, Neptune is forced by Nepgear to go out and work by herself. It is then that Neptune runs into Rei for a second time who is still lost. Neptune, trying her best to prevent Rei from being upset, ends up only angering her further which results in Rei sending Neptune to the Ultradimension. Rei is surprised and believes she has made Neptune disappear and begins to laugh.
Neptune finds herself in the Ultradimension after falling from the sky and landing on Noire. She meets a girl named Plutia who claims to be the CPU of a recently chartered nation by the name of Planeptune. Neptune is surprised by this since to her knowledge she is the CPU of Planeptune. She tries her best to convince Noire and Plutia that she is a CPU but is unable to do so after finding out that she can't even transform. Upon learning that humans can become CPUs by using a CPU Memory, Neptune decides to find one with Noire and reattain her ability to transform (and also to prevent herself from aging). The Seven Sages, who are alerted by Rei that Planeptune has another CPU, sends Abnes to go check things out; only for her to see that Neptune isn't a CPU and thus believing the information to be false.
When the Histoire of the Ultradimension makes her appearance, she states feeling a connection to Neptune despite having no recollection of ever meeting her prior. Neptune explains her situation to Histoire which leads her to concluding that Neptune is from another dimension. In order to see if this is valid, Histoire attempts to contact the Histoire in the Hyperdimension to see if what Neptune says is true. Though, she mentions that process will take three days.
Noire makes her way to Zeca Ruins No. 1 in the hopes of finding a CPU Memory from the Memory Core. Neptune follows her, wanting to obtain a CPU Memory as soon as possible and Plutia naturally tags along as well. When they arrive they are met with Arfoire and Pirachu who have two CPU Memories from the Memory Core with them. Noire, not wanting to let this one chance slip her by, tries to take them by force with Neptune following after her. Arfoire gives the CPU Memories to Pirachu so he can escape with them while she deals with Neptune and Noire. However, Pirachu is followed by Plutia who ends up transforming and taking the CPU Memories away from him.
Neptune and Noire find themselves unable to defeat Arfoire until Plutia arrives with the CPU Memories and hands them over in exchange for Neptune and Noire agreeing to do something for her. Neptune and Noire successfully become CPUs and take down Arfoire easily. Arfoire swears to get revenge and flees afterward. The girls head back to the Basilicom where it is revelead that Neptune had been telling the truth all along. The Hyperdimension Histoire is unable to immediately provide a solution as to how Neptune get home which results in Neptune being stuck in the Ultradimension until further notice. Now being a CPU, Noire goes out to found her own nation while Neptune stays with Plutia in Planeptune.
Three years have passed in the Ultradimenson. Noire has founded Lastation and has taken a considerable amount of shares from Lowee, which ultimately causes bad blood between the two nations. Histoire kicks Neptune and Plutia out of the Basilicom so that they can visit Noire in Lastation and learn how to work like proper CPUs. Noire teaches them how to use the Scout System and the two head back to tell Histoire about it. However, since they didn't learn anything else, she sends them right back to Lastation. The Seven Sages organize a meeting to talk about Lastation's unprecedented growth and try to figure out a way to deal with it.
Abnes heads to Lowee to inform that the CPUs of Planeptune are in Lastation and possibly learning ways to develop their own coutry. She goes on to say that it is possible that if Planeptune experiences growth similar to Lastation then they will take the remaining bit of Lowee's shares. Enraged, Blanc heads to Lastation to confront Neptune, Plutia, and Noire but soon realizes that she didn't think things through and has no real reason to even be there in the first place.
In order to prevent the CPUs from fighting and possibly starting a war, The Seven Sages send Copypaste and Pirachu to a Lastation factory to destroy it so that Noire's attention will be taken away from Blanc. Noire, Neptune, and Plutia make their way to the factory to deal with the threat, but not without Noire telling Blanc not to cause anymore trouble beforehand. Copypaste and Pirachu trick Noire into believing that Blanc was only in Lastation to serve as a distraction so that The Seven Sages could destroy the factory. This leads to her assuming that Blanc is working with The Seven Sages while Neptune believes otherwise.
Neptune and Plutia return to the Planeptune Basilicom and receive contact from Histoire in the Hyperdimension. It is established that for every day that passes in the Hyperdimension, a year passes in the Ultradimension. In order for Neptune to return home, Histoire states that she must increase Planeptune's shares. After this, the connection is severed.
Noire comes to the Planeptune Basilicom to complain about Lowee and The Seven Sages. Plutia grows irritated of Noire's complaints and transforms, giving her a “lecture” to convince her to go to Lowee and voice her complaints directly to the CPU. After Noire gets out of her traumatized state, she, Neptune, and Plutia head to Lowee by running past the border patrol unit. When in Lowee Plutia, who is lost, bumps into Vert. When Neptune and Noire finally locate Plutia, Neptune nearly exposes Vert's identity as the CPU of Leanbox until Vert tells her to keep it a secret.
The girls, along with Vert, make their way to the Lowee Basilicom where they are met with Blanc, Mr. Badd, Abnes, and Pirachu. It is revealed that their fight will be broadcast live on TV so that everyone can see Blanc defeat the other CPUs. Vert quickly makes her getaway due to not wanting to be seen on TV. The remaining CPUs face off against Blanc, ultimately winning. This plays directly into The Seven Sages plans as they never expected her to win in the first place. With Blanc's defeat broadcast live to her entire nation, she suffers an extreme decrease in shares. Mr. Badd uses this to take over her nation while imprisoning Blanc and the others due to them being too weak to fight back.
While incarcerated, Plutia talks with Blanc and eventually tells her that she and the others will be her friends and will also help take back her nation. Vert arrives with the master key to the cell and lets them out. Now being free, the party makes their move to stop Mr. Badd by broadcasting his defeat live during his speech. When they all transform to prepare for battle, Blanc is the only one who cannot due to not having enough faith. Neptune, Noire, and Plutia give Blanc their own faith which is just enough for her to transform. Together, the four CPUs take down Mr. Badd and have him expose his evil deeds live on television. After that, Blanc thanks Neptune and Plutia for their help, not wanting to thank Noire for being so rude to her beforehand. Blanc says that maybe she'll come to Planeptune to see Plutia after she's finished restoring her nation, and Neptune, Plutia, and Noire all head home.
In the Hyperdimension, Nepgear and Uni are out on Patrol in Planeptune due to the citizens group acting weird. The two of them notice the Rei of their own dimension walking around and go to confront her. Uni immediately asks why Rei is there and also states that she has various citizen group questions. Instead of answering her questions Rei states that “piddling little silver spoon babies” shouldn't try to touch her so thoughtlessly and hits Uni before suddenly vanishing. Alone, Rei says that she will not stoop so low as to deal with CPU Candidates since her targets are the CPUs themselves.
Back in the Ultradimension, The Seven Sages are having another meeting to discuss their next course of action. With Lowee being restored and now having a relationship with the other two nations in addition to the evil deeds of the Sages being exposed, they are now between a rock and a hard place. The group spends most of the meeting arguing and after Abnes leaves to go confront the CPUs, it is revealed that they still have another ambiguous plan which is going smoothly.
In Planeptune, Neptune and Noire arrive together after spending time together for two weeks in Lastation. Blanc arrives as well and she and Noire instantly begin to fight. Neptune quells the argument by telling them that if they fight in the middle of the street then Plutia will see and they may be faced with Iris Heart. Not wanting to deal with Plutia's sadistic goddess form, they immediately stop and head to the Basilicom together. Upon entering the Basilicom they are greeted by Plutia and a group of babies. Initially they don't question why the babies are there but when they do they quickly begin to question Plutia. Histoire appears and explains that due to the missing children cases in Planeptune that the Basilicom is acting as a daycare. Not wanting to have anything to do with children, Noire and Blanc attempt to leave. However, when Plutia says she might end up transforming because taking care of them all alone is, they stay.
Histoire comes back with news of Leanbox declaring war against the other three nations and also with news of the other Histoire having finally found a way to bring Neptune back. The group heads to courtyard where Histoire opens the path back to the Hyperdimension. Before Neptune can even walk through, Nepgear gets dragged into the portal and ends up landing on the Ultradimension Noire. With both Neptune and Nepgear in the other dimension, the Hyperdimension Planeptune is at even higher risk of losing more shares. In order to reopen the path yet again, Histoire requests for Neptune and Nepgear to gain even more shares in the Ultradimension Planeptune before disconnecting.
Neptune and the others head for Leanbox to meet with the CPU and leave Nepgear to take care of the children. They travel to Leanbox by using a boat that was prepared by Vert. Upon arriving they head to the Leanbox Basilicom where Vert declares war, not with violence, but rather by taking all their shares the fair way with her superior console. Not threatened by her claims, Neptune and the others all return home.
A week later, Vert storms into the Planeptune Basilicom accusing the other CPUs of spreading false negative rumors about her console. When Neptune and the others explain that they didn't do anything and that people genuinely think her console isn't all that great, Vert challenges the other CPUs to battle in the place where she found her CPU Memory. Neptune thinks this is a good opportunity to try and get any spare CPU Memories Vert may have for Nepgear and decides to go with the others.
When they arrive, Neptune and Plutia explain the situation to Vert and Nepgear manages to receive a CPU Memory so she can become a goddess again. Vert then tricks Nepgear into believing she is her sister due to them using a CPU Memory from the same core. Neptune and the others face off against both Vert and Nepgear and ultimately win. After this, a Leanbox soldier arrives and tells Vert that The Seven Sages are wreaking havoc in Leanbox. Due to Vert being injured from her fight against the other CPUs, Neptune and the others offer their help in defeating the threat.
The group heads to Leanbox where they find both Arfoire and Copypaste destroying the city. The CPUs make quick work of the two but are unable to catch them after they flee. Vert formally thanks Neptune and the others for their help and says she will repay the debt she owes after focusing on her nation for bit. In the conclusion of the chapter, it is revealed that Vert sneaks into the Planeptune Basilicom every day to see Nepgear and that the Basilicom in general has become a hangout spot for all the CPUs.
In Planeptune's Basilicom, Noire, Blanc, and Vert receive calls about trouble brewing in each of their nations. The three of them immediately leave to deal with the trouble in their own lands. While initially Neptune wanted to let them deal with their own problems, she is convinced by Histoire, Plutia, and Nepgear to go and assist the other nations.
In Lastation, the three Planeptune goddesses make their way into Noire's Basilicom to see how she's doing. Nepgear finds a camera hidden in her room and comes to the conclusion that someone is taping her. She uses a special device to track where the data is being sent to which leads them to Anonydeath who claims that everything he did was for Noire's love. Anonydeath teases Noire which makes her upset. Noire, Neptune, Nepgear, and Plutia all transform and face off against Anonydeath. Once he is defeated, he ensures his escape by tricking Noire into thinking that doing anything will trigger a program that will make all of his videos of Noire go viral only for her to find out that it was all lie in the end. With the culprit in Lastation dealt with, Noire returns Lastation to deal with aftermath of Anonydeath's actions.
When Neptune, Nepgear, and Plutia head to Lowee they go to the Basilicom and see that things are going better than expected. Blanc explains that the damage was minimal and that Copypaste was destroying her Basilicom before she came back but ended up working at the Mines when he learned he could destroy as much as he wanted. Ever since, Mining has been going exceedingly well. However, Blanc is still upset at what he did to the Basilicom and so she and the others head to the Mines to see Copypaste. When they arrive they see that all the mine workers love him and when they beat him up they show some resentment towards Blanc. The moment they see this, Neptune and the other two Planeptune goddesses make a run for it and leave Blanc to deal with the situation herself.
Upon arriving in Leanbox, Neptune, Nepgear, and Plutia are faced with a strange looking creature. Suddenly, Green Heart appears and asks for their help in defeating the strange monster but they fail in actually stopping it. The girls are initially hesitant to help Vert deal with monsters due to how disgusting they were but Vert manages to convince them to help by saying more might spawn in Planeptune if they don't deal with the threat now. They follow the creature all the way back to Mr. Badd who is revealed to be the culprit behind the strange creatures' appearance in Leanbox. They end up fighting both Mr. Badd and his three strange creatures. When they defeat them, Mr. Badd and the creatures escape.
Neptune, Nepgear, Plutia, and the other CPUs all rendezvous back at the Planeptune Basilicom where they find Histoire stuffed in the trash and trapped between her book. When they get her out she explains that The Seven Sages have kidnapped Peashy, IF, and Compa and says that they are taking a road towards Lowee. After hearing this, Neptune and the rest of the group immediately head out to save them.
They arrive to Haneda Mountain range where they find Pirachu and Compa. Before they can do anything to Pirachu, Compa saves him by saying that he was going to take her back to the Basilicom. Out of fear, Pirachu tells them where Arfoire went and the group goes off in the direction he had directed. The group quickly finds Arfoire with IF and takes her down with Iris Heart inflicting torture upon the villain after and subsequently traumatizing IF.
Meanwhile Peashy is with Rei and is complaining about wanting candy. This leads to her rummaging through Rei's purse and finding something to eat. When the group returns to the Planeptune Basilicom after being unable to find Peashy they are greeted by both her and Histoire. Peashy explains that the lady who took her offered her candy but when she didn't get any she got bored and left. This relieves everyone and with the crisis finally resolved, the group assembles a sleepover in the Planeptune Basilicom.
At The Seven Sages base, Anonydeath calls forth a meeting to reflect on their failures. Abnes overhears their talk about kidnapping children which enrages her. She demands to know the location of where the children are being held and when she doesn't get her answer she leaves stating that she will find the children herself.
In the Planeptune Basilicom, the goddesses are having a meeting of their own. Nepgear explains that they had recently been contacted by the Histoire of the Hyperdimension and that the situation in their dimension was getting worse. Neptune requests the help of the other CPUs to increase their shares. While initially they are hesitant on the idea, everyone decides to pitch in and help increase Planeptune's shares so Neptune and Nepgear can return home.
Anonydeath visits the Basilicom posing as Peashy's father. The CPUs are shocked when they hear this and express immediate distaste towards his supposed reasons for abandoning Peashy in the Basilicom all those years ago. Neptune and Peashy get into an argument and Peashy leaves with Anonydeath, still upset at Neptune for being mean to her “dad.”
Abnes visits the Basilicom to request the CPUs' aid in freeing the abducted children. At the first they do not believe her due to her being a member of The Seven Sages who were the ones responsible behind the kidnappings in the first place. Abnes states that she left The Seven Sages and had no knowledge of their actions because if she did she would have tried to prevent it. Plutia trusts Abnes' words and everyone else eventually falls in suit.
When they make it to the where the children are being held, they see the strange creatures who were in Leanbox with Mr. Badd not too long ago. As they search for the children they see Mr. Badd himself along with the strange creatures and demand to know where the children are being held. When Mr. Badd doesn't comply they fight him and the strange creatures only to later find out that the creatures are in fact the children they have been looking for and that each child had a CPU Memory forced on them. While they wished to take down Mr. Badd once and for all after hearing this, they merely flee due to knowing the children will protect him.
Once they exit the base, they are encountered by another CPU who claims to go by the name of Yellow Heart. She attacks the group and despite their efforts she easily defeats them all, being powerful enough to knock them all out of goddess form. She flies away shortly after this and the CPUs, defeated, return to the Basilicom where they see a broadcast on television declaring the founding a new nation known as Eden lead by Yellow Heart.
Ten years have passed since the creation of Eden and each of the nations have suffered a major decrease in shares. The group meets in Lowee's Basilicom to discuss what they can possibly do to combat this situation but none of them have any ideas. Copypaste, who has been rebuilt to serve as the tea server in the Basilicom, notifies them of The Seven Sages stirring up trouble outside of town. The CPUs act with haste to go deal with situation. They make their way outside of town and see some weak monsters and not any real threat. The party deals with this swiftly and all end up going to Planeptune's Basilicom after. In Eden, The Seven Sages are conducting yet another meeting. Arfoire is displeased at having to serve under a CPU and says that she is cutting ties with the organization so she can do as she pleases.
In Planeptune, the party arrives and eats a meal prepared by Compa. Histoire arrives shortly after and talks about how she's doing her best to gather intelligence on Eden and their plans while also finding and calculating the damage caused by the founding of the nation. Plutia suggests that they all help Histoire out in finding information to which everyone agrees to due to not having anything better to do. IF goes out on patrol to find information and bumps into Arfoire and Pirachu. Arfoire, wanting to take down the CPUs, kidnaps IF as a way to bait them to her.
The party returns to the Basilicom after running errands. Histoire frantically informs them that Arfoire has kidnapped IF and requests that the CPUs meet her in a specific place to get her back. Knowing full well that this is most likely a trap, Neptune and the others head out to rescue IF. When they arrive at the specified location they are met with both Arfoire and Pirachu who have the captured IF. Pirachu tries to convince Arfoire to run but she insists on staying and fighting. However, seeing Plutia's anger makes strikes fear into both of them and Pirachu tells Arfoire to run, saying he'll buy time for her. Surprised, but refusing to show any gratitude, Arfoire complies and runs. The CPUs are stricken with awe at Pirachu's display of friendship and have no intentions of actually fighting him until Plutia transforms which ultimately forces them to battle him as well.
After being defeated by the CPUs, Pirachu is taken back to the Planeptune Basilicom and is nursed back to health by Compa. The CPUs interrogate him on information about Yellow Heart which he is hesitant to give until Compa begs him to help them out. Pirachu reveals that Yellow Heart's body was altered to channel power from other locations which is the reason behind her immense strength. He also tells them the location of where Anonydeath is harboring the device that allows her to do so. Neptune and the others deduce that by destroying the machine that Yellow Heart will be as strong as a normal CPU.
The CPUs head to Anonydeath's lab where they confront him head on. Despite his efforts to stall, the CPUs all transform and make quick work of him and destroy the machine after. Yellow Heart arrives on the scene, unaware that the source of her power is now gone, fights the CPUs to defend Anonydeath. Upon her defeat she reverts back to human form, revealing herself to have been Peashy all along. Due to having her memories altered, she does not remember any of them. However, when it seems like Peashy is starting to remember them, Anonydeath tricks the CPUs by telling them the facility will blow in one minute before making off with Peashy. The party makes haste in escaping but soon realizes that they were tricked. Neptune, upset at the discovery of Yellow Heart being Peashy and her memories being altered, vows to get her back.
The CPUs assemble Abnes, Copypaste, and Pirachu at the Planeptune Basilicom to learn the location of The Seven Sages' main base of operations. Vert states that the matter of restoring Peashy's memories lies with Neptune and Plutia. Neptune says whatever happens, happens and Nepgear concludes she has no basis whatsoever. Blanc says that maybe if they smack her head hard enough, Peashy's memories will return. Neptune says that it's a good idea and decides to go with that. Noire disagrees, but Plutia says it'll all work out. IF and Compa are doubtful of the plan's success, but everyone heads out anyway.
Meanwhile, the remaining members of The Seven Sages conduct a meeting. Due to Peashy nearly recovering her memories of the others in their last encounter with the CPUs, Anonydeath resealed her memories with a spare machine which put her in a deep sleep. Anonydeath predicts that Yellow Heart will be waking up soon and Mr. Badd says that he'll stay in the shadows and spend time with his daughters.
When Yellow Heart finally awakens, Anonydeath sends her out to deal with the CPUs. They find Peashy, and are surprised to see she's sleeping. Peashy wakes up and notices the CPUs, remembering she was told to deal with them. Since Peashy still doesn't remember who they are, they decide to make her remember by using force. She is defeated by the other CPUs and reverts back to human form. Instead of remembering them as they had hoped, she begins to cry and bawl.
Peashy continued to cry and throw a tantrum for hours and when she finally wore herself they took her back to Planeptune. However upon finding herself in a foreign place, she began to scream and cry all over again. It took several days for Peashy to calm down. Afterwards, things returned to normal, but Peashy still didn't remember them. Instead of returning home like they were supposed to, Neptune and Nepgear refuse to leave the Ultradimension until they are able to restore Peashy's memory.
The CPUs assemble Abnes, Copypaste, and Pirachu at the Planeptune Basilicom to learn the location of The Seven Sages' main base of operations. Neptune says she has top secret plan to help Peashy recover her memories and Compa and IF request to go rescue Peashy as well, promising they won't hold them back. Neptune and Plutia agree and with that settled they head out to save Peashy.
Meanwhile, the remaining members of The Seven Sages conduct a meeting. Due to Peashy nearly recovering her memories of the others in their last encounter with the CPUs, Anonydeath resealed her memories with a spare machine which put her in a deep sleep. Mr. Badd is tasked with the job of making sure the CPUs do not find the base. Mr. Badd accepts this, saying it will be his final act of public service.
When the CPUs arrive to The Seven Sages' base they run into Mr. Badd who fights them without the aid of his “daughters.” Mr. Badd is ultimately defeated by the combined power of the CPUs and his daughters appear, begging them not to kill their father even though they never planned to in the first place. The monsters explain how Mr. Badd treated them kindly as if he was their real father and that he was also looking for a way to turn them back into their human forms. While the CPUs still can't forgive Mr. Badd for turning the girls into monsters in the first place, each of them offer to aid him in his goal. With this out of the way, they continue to their search for Peashy.
Anonydeath, having monitored the entire conversation between Mr. Badd and the CPUs, and sends Peashy out to deal with them. When they find Peashy, they are surprised to see she's sleeping. Peashy wakes up and notices the CPUs, remembering she was told to deal with them. IF and Compa try to jog her memories by saying they spent their childhood together, but Peashy doesn't remember anything. Neptune transforms into Purple Heart and says that they need to weaken her so that their plan to restore her memory will be more effective.
After defeating Yellow Heart, she reverts back to her human form. Neptune and Plutia also revert back and go through with what they planned. They initiate the five-item set plan that contains five key items from Peashy's time in the Basilicom. Their plan fully works when Neptune shows Peashy the picture she drew of everyone living in the Basilicom, fully jogging her memory. Cheerfully, Peashy headbutts Neptune and everyone welcomes her back
Due to Peashy recovering her memories and The Seven Sages being reduced to only two members, the organization disbands. Croire appears shortly after this, and Rei tells her she's going to go and apologize to the CPUs after realizing everything she did was wrong.
The party returns to the Planeptune Basilicom with Peashy and Histoire welcomes her back. The group decides to take a break and relax, discussing what will happen next. With The Seven Sages gone and Eden no longer a threat due to Peashy being back with them, they no longer have anything of major importance to do. Neptune and the others decide to head out to do some work, inviting Peashy to come with them.
Meanwhile, Rei is lost in the forest on her way to apologize to the CPUs. Croire gives her back the dark power than had been given to the other Rei. She completely changes and decides retracts her previous intention of apologizing, making a clone of Purple Heart to send to them so that they will come to her instead.
The Purple Heart clone arrives to the Planeptune Basilicom when everyone is there and begins to stir up trouble. They quickly defeat her and begin to ponder on where the clone came from. Neptune deduces that Rei Ryghts is possibly behind it, due to the one of her world possibly being the reason she was sent in to the Ultradimension in the first place. They decide to ask the former members of The Seven Sages for information regarding Rei.
They gather the former Seven Sages in the Lastation Basilicom and ask them if Rei has any powers that she would use for evil. Each of them respond negatively. However, Anonydeath contacts them and informs them that Neptune's gut feeling is actually accurate. He states that Rei is using him as CPU bait to lure them to her. Noire refuses to go until she hears that he's surrounded by clones of her which acts as her incentive.
Upon making there way to the location where Rei is, they encounter a fake White Heart, Green Heart, and Yellow Heart. Once they defeat them and make their way further into the dungeon they find Anonydeath surrounded by four Black Hearts. When they are dealt with, Anonydeath thanks them and warns the CPUs that Rei in her current state is possibly just as strong as them before leaving.
The party finally reaches Rei and are greeted by her psychotic rambling. They all transform, ready to deal with her only for Rei to transform as well and reveal her goddess form. When they defeat her she immediately reverts back to her human form and faints. They are surprised to see that she was able to transform just like them. The party decides to take her back with them for an interrogation.
In the Hyperdimension, Rei hysterically laughs at the fact that the her in the Ultradimension was defeated by the CPUs. Having gotten even stronger, she states that she can easily destroy one or two worlds with no problem and says she will in due time after paying her useless impostor (Ultra-Rei) a visit. Back in the Ultradimension, Rei awakens and the party immediately begins to question her about her ability to transform. Rei admits to being a CPU and explains the history of Gamindustri's past. She states that in the past, Gamindustri was chaotic and lawless. When she became a CPU she created the nation know as Tari. Initially she had tried to lead the people as best she could but eventually the people rose against her and she ultimately destroyed her nation. Because of her mistake, she felt as though the problem lied in all CPUs and thus formed The Seven Sages.
Vert asks how Rei found power great enough to stand against them. Rei suddenly panics, saying nothing has been resolved at all. She mentions the other dimension and sates that she gave her power to the Rei in the Hyperdimension. Vert asks yet again how she found such great power, and Rei says she doesn't quite know herself. Vert then asks how Rei know about the other her that existed in the Hyperdimension. Rei explains that her power allows her to distort or even pierce other dimensions. Just as she mentions Croire, she appears and Vert concludes that Croire was the one who took the power over to the Hyperdimesnion after learning she can travel to other dimensions. Croire tells the group that the other Rei plans to destroy the world and says it'll all be happening soon. Just as she finishes her sentence, the event starts and Croire takes her leave. The CPUs make haste in returning to their own nations to lead their people to safety. When they return to the Planeptune Basilicom, the Histoire in the Hyperdimension contacts them and tells Neptune and Nepgear to hurry home as the situation has gotten worse.
When preparations are complete Histoire proceeds in opening the path, telling them to imagine releasing all the shares they have gathered so far. She is surprised to see that there are so many shares and says they will definitely succeed. When the path is opened, Neptune and Nepgear say their final farewells to the others. Just as they are about to leave, Plutia glomps Neptune which results in them both falling through the light and leaving Nepgear behind.
Once Neptune and Plutia arrive to the Hyperdimension, they are met with Uni, Rom, and Ram who are expecting to see Nepgear but end up heavily disappointed. Histoire arrives not too long after and explains the situation to them, saying that Planeptune has taken major damage and that the other CPUs have gone ahead to deal with the matter.
Upon arriving to the city center, Plutia gets upset at seeing what the city has become. Neptune tells Plutia to transform so the candidates can be 'broke in' and not freeze up during the final battle. Plutia agrees, and transforms into Iris Heart. She then proceeds to 'have fun' with them which leaves them all crying and scarred after. In the midst of this, the Black Heart, White Heart, and Green Heart of the Hyperdimension are in the middle of fighting Rei who claims to be only toying with them despite the situation looking to be in their favor.
Just as they make it to Rei, they see the Hyperdimension CPUs have been defeated by her. Neptune and the others are upset by this and transform ready to fight her despite Rei's overconfidence. With the Candidates help, Neptune and Plutia defeat Rei. However, Rei gives her dark power over to Croire to take away. When Croire is asked what she plans to do with that dark power, she states that she's going to another dimension where they don't exist, and then leaves. This resolution leaves both Neptune and Plutia unsatisfied. A few years have passed in the Ultradimension and Nepgear is still stuck. She yells at Neptune and Plutia during a call between the two Histoire's trying to tell her that even though its been a few days for them in the Hyperdimension, it's been years for her. Neptune says that Nepgear's seems to really be suffering over there and asks Plutia if she wants to start working for real. Plutia answers by saying maybe after another nap, which makes Nepgear yell at them again to bring her home.
When preparations are complete Histoire proceeds in opening the path, telling them to imagine releasing all the shares they have gathered so far. She is surprised to see that there are so many shares and says they will definitely succeed. When the path is opened, everyone is shocked to see how huge it is. Hyper-Histoire concludes that with the path this size, everyone can travel to and from the dimensions as they please. Just as they are about to enter, IF questions what will happen to the Ultradimension with all the CPUs gone. Suddenly Copypaste appears and says to leave everything to them.
Anonydeath intercepts the connection between the two Histoires and states that he will repay the CPUs by helping them out. He says the Mr. Badd will watch over Lastation and the other two are on their way. Abnes and Pirachu show up and assure them that they will help take care of the Ultradimension Gamindustri under Rei's command. The party then heads through the path and ends up in the Hyperdimension. The party heads to the Planeptune Basilicom and are welcomed by Histoire. Just as Histoire is about to summarize the situation, the CPU Candidates arrive and are delighted to see Nepgear. Uni, Rom, and Ram are surprised to see the Noire and Blanc from the other dimension and the two parties get wrapped up in their own conversations. Thirty minutes pass and Histoire is finally able to explain the situation to them. After learning the other CPUs are dealing with the clones inside the city, Neptune her party head out along with the Candidates.
When they make it to the city center, they encounter the Hyperdimension Noire who has been stuck opening a hole through the barrier so people can escape. When she tries to get someone to switch with her, everyone ends up abandoning her. The party then runs in the Hyperdimension Blanc and Vert who are fighting the clones. An Iris Heart duplicate appears and Plutia is happy to have a clone of herself finally. After defeating the fake Iris Heart, the Hyperdimension Vert and Blanc say that they'll hold off the copies while Neptune and her party go ahead and deal with Rei. When they make it to her, Rei gives them a psychotic lecture on why CPUs shouldn't exist. Figuring that talking to her would be a waste time, everyone transforms and decides to deal with her by using force.
As they face off against Rei, they find themselves tired out due to her strength. Suddenly the Rei from the Ultradimension arrives, stating that she can't sit around while pushing her problems onto someone else. She tries to convince her other self to stop what she's doing but the other Rei refuses. Croire, takes the power the Ultra-Rei brought over and uses it to power of the Hyper-Rei. The Ultradimension Rei says that no matter how many times they defeat the Hyperdimension Rei, that they will still have to do something about the dark power.
The CPUs are forced to face Rei for a second time and after defeating her the dark power comes out. Iris Heart tries to tame the dark power with the Ultradimension Rei's help. Both Iris Heart and Rei take some of the power and successfully subdue it. With the problem now resolved, everyone heads back. Croire watches them all leave and ponders on where she should start trouble next.
Three months pass and both worlds go back to being peaceful, however the pathway between the dimensions seems to be open forever. The Hyperdimension CPUs and Ultradimension CPUs (with the exception of Noire) causally pass between the path and casually spend time with their other selves. Anonydeath helps the girls who had been turned into monsters go back into their human forms, and Arfoire runs an eggplant farm with Pirachu as her helper.
As for Rei, in the Ultradimension she reforms The Seven Sages as an organization meant to help the CPUs, and in the Hyperdimension she is forced to preform community service for all the damage she caused. Neptune, Plutia, Compa, and IF end up being trapped in the enormous amount of dolls that Plutia had made of all her friends and Peashy and Nepgear show up in the middle of it. The story ends with Croire being captured by an unknown individual who sounds like a much younger Neptune.