Histoire recalls about the Console War. Humans below in Gamindustri bring power by faith through the CPU that resides in Celestia, who in turn gives them protection until the former goddess and Histoire broke the balance and split it into four CPUs. Celestia lost its tranquility, and the CPUs began to fight over the honor of ruling over the world. Histoire blames herself for being the cause but can't do anything about it, but she hopes the CPUs's destinies will save them from "her scheme."
After "Opening" event
Lasting over thousands of generations, the CPUs keep on fighting over the title of True Goddess. Green Heart comes up with an idea to eliminate or exile one of them for a change. Green Heart, Black Heart, and White Heart decides to team up and exile Purple Heart. Feeling confident, Purple Heart stands up against the three of them.
After "Opening 2" event
Neptune finds herself somewhere in the dark and wonders where she is. Momentarily, Histoire's voice reaches Neptune's ears. Histoire introduces herself as the tome that assisted the goddesses of Celestia for generations, explains that Neptune isn't dead, that she created her, and that she's locked away somewhere. Histoire asks Neptune to help her with the mistakes she made.
Histoire's Cry 2
After "Histoire's Cry" event
From the blaring alarm clock, Neptune wakes up in someone's bedroom. The owner arrives and explains that she ensconced Neptune to her room after she found the girl, who fell from the sky. She introduces herself to Neptune as Compa, a nurse-in-training. Neptune also gives Compa her name. Having a hard time pronouncing her name, Neptune lets Compa pick a nickname for herself, so Compa settles with "Nep-Nep" as Neptune's nickname.
Compa + Amnesiac
After "Histoire's Cry 2" event
Compa decides to diagnose Neptune and bandage her up. Using all the bandages, Compa bandages Neptune up too tightly. After struggling to escape from the bandaging, Neptune decides to bandage her body all by herself.
Compa + Amnesiac 2
After "Compa + Amnesiac Event" event
Neptune wonders where she is, so Compa tells her that they're in the Central City of Planeptune, one of the four major landmasses below Celestia. With Neptune not remembering anything, Compa diagnoses her as an amnesiac. Neptune remembers someone asking her for help on her dreams and explains it to Compa. Compa explains that monsters are ravaging the landmasses and that the military can only keep them at bay. Neptune concludes that it's her mission to "defeat the boss generating the monsters" and to save the world. Reasoning with herself, Compa decides to tag along with Neptune on her "mission." Even though she agrees, Neptune worries about Compa's nursing school, but Compa explains that the monsters caused the schools to close. Finally they leave for a dungeon.
After "Compa + Amnesiac 2" event
Compa leads Neptune to a dungeon filled with weak monsters. Disappointed, Neptune decides to wait until Compa finds the boss, but Compa retorts that the goddess will punish Neptune for "abandoning the party." At the mention of "goddess," Neptune becomes amazed. Compa explains about the other landmasses besides Planeptune, which are Lastation, Leanbox, and Lowee, how they're each ruled and governed by a goddess, and how the people go to the Basilicom to worship them. She also explains that nobody knows where the monsters are coming from. The people come to the conclusion that it might be due to the CPUs' weakening powers. They put the questions aside and start hunting the monsters within the dungeon.
First Dungeon 2
Defeat "Guard Vermin (Planeptune)"
In front of Compa, Neptune reverts from HDD form back to her human form. Neptune hears Histoire's voice and speaks to her. Since Compa can't hear Histoire's voice, Neptune tells her that she will relay Histoire's words to her after. Wondering about the item she found, Histoire clarifies that Neptune found a Key Fragment that will release the tome from her seal. She also asks Neptune to find the other three Key Fragments from each landmass, guarded by a strong adversary somewhere. Neptune explains that the ambition to save Histoire is only a "bore-chore" and that she'd rather do it to save the whole world, so Histoire explains that saving her is equivalent to saving the whole world due to her being "the world's everything." Neptune accepts the aspiration, so Histoire goes through more detail. After their conversation, Compa feels left out and becomes sad. As they leave the dungeon, Neptune decides treats her to something to eat and relay Histoire's message.
Having gathered the Key Fragment in Planeptune, Neptune wants to go travel to the next landmass, but Compa explains that the place is still infested by monsters. Neptune reluctantly agrees to stay and "clobber some more monsters."
While traversing the dungeon, Neptune accidentally runs into a girl, who fell on the ground afterwards. The fallen girl introduces herself as IF, who was requested by the Basilicom to eliminate the monsters in the same dungeon. The girls introduce themselves to each other. Neptune puts Compa in charge of item inventory after hearing her say that she's good with it arts, crafts and math. Neptune offers to work together with IF, so IF agrees as she sees it to make her job easier. Compa cheerfully says that they're a party and are together forever, but IF says that she's only joining them for the dungeon and that the two are joining her. When Neptune says that Compa is joining Neptune discourages the idea and says that it's against the rules to abandon the party, but IF says that it doesn't matter.
Neptune explains to IF that they're looking for Key Fragments to free Histoire. After reinterpreting what she heard and seeing the logic behind it, IF decides to tag along with Neptune and Compa as they find the Key Fragments. IF explains that she could help them locate where the Key Fragments are. They head to Planeptune's Basilicom to get some clues to where the monsters guarding the Key Fragments are located and to get a permit to travel to other landmasses via the Sky Harbor.
The newly formed group head to Planeptune's Basilicom. Asked by IF, Neptune goes inside the Basilicom to ask for permission to travel to other landmasses. When asked for a reason to Terraport, Neptune explains that she and her party will defeat monsters. The staff sees it as an admirable reason and gains permission. Not knowing about the Basilicom, Neptune asks the staff member about it. The staff member explains its origins and how it functions. After their conversation, Neptune leaves and goes back to Compa and IF.
Despite being a new member in the party, IF complains that they should go and find the second Key Fragment, but Neptune and Compa insists that they should help Planeptune with its monster situation first.
The group arrives at Planeptune's Sky Harbor. Seeing a split on the ground, Neptune assumes its cause was from an epic war a long time ago. Wondering what Neptune's babbling about, Compa explains to IF that Neptune has amnesia and that she found her from the ground and treated her a few days ago. IF becomes surprised from how Compa found Neptune. IF also tells Compa that she's too formal with her and that Neptune is too friendly with her. Compa then explains to Neptune about how the Sky Harbor works. IF also explains that the permit they got allows them to Terraport anytime.
The party arrives in Lastation's Basilicom to find information about monsters and the Key Fragment. Moderator, a staff in the Basilicom, discourages the girls and says that not even Lastation's Defense Force can handle the monsters. Moderator dismisses the party for "being nothing but a bunch of girls," but the party persists. Seeing it's no use, the group leaves.
Available after seeing "Basilicom Revolution 3" event
The group finds someone who asks them to fight monsters. They meet Chian, the one asking them the favor. Asking the girls to handle some monster who are attacking Passe's carriages and trains, the group complies.
Finish "Windy Wasteland: Den by Merchant Way" dungeon
After defeating the monster within, the party wonders why they're so many of them. IF explains about how the monster attacks shake the faith of the people, decreasing the protection power of the CPUs. Neptune, in HDD form, assures that she's the only one who can save the world.
The group receives a "dinky" reward for completing their objective. Compa and IF explains that it's because of Avenir's monopolization but that it's not the only reason. Neptune comes up with the idea that Avenir is an evil corporation and plans to take it down. IF tries to sway Neptune off the idea and warns them that their budget might run out if they don't stick to their main objective.
Neptune, Compa, and IF gets cozy in Chian's home. Chian explains that she had to get two jobs due to Avenir. Neptune sees Avenir as evil and so does Chian. Neptune plans to defeat Avenir for Lastation to find peace. Chian assures that her business won't go down and explains about the Technology Expo, a showcase of technology from various companies. Chian plans to win at the Expo and meet to negotiate with Black Heart afterwards. Chian asks group to help her and Passe to eliminate some monsters to help with progress on Passe's prepping for the Expo.
The group meets their client from Avenir. Compa introduces her and the others to Singe, their client. "Having no other choice," Singe gives the girls the objective of defeating the surrounding monsters and preventing them from damaging Avenir's facility. Compa sees Singe's attitude as being rude and thinks that he's underestimating them. IF sarcastically explains that it's probably due to Compa and Neptune looking like little girls. Compa retorts and points out IF's physique.
The party defeats the monsters as Singe's requested them to. Singe acknowledges the request done but warns the group that Avenir will never conduct business with them if even one monster damages their facility. Compa suggests that he could just fix it if ever damaged, but Singe retorts and harshly lectures her about how machines are more precise, unlike humans. He warns her that he'd rather make machines do the work than humans if they're expected to make mistakes. Compa becomes daunted and whimpers. IF explains that she didn't do anything and becomes mad thinking that Singe mocked humanity.
The group comes back to Chian's home. Neptune relays Chian about their job and how Singe made Compa cry with his lecture. Chian explains how she met Singe before and how he favors machinery rather than manual labor. After that, Chian gives the girls the job of retrieving shop materials from Chevre. Suddenly, a radio broadcast from Lastation's Basilicom announces that the Tech Expo is cancelled.
The trio wonders what they should do with the job they accepted from Chian. They were given the mission to rescue a child from a monster. On the other hand, IF just wants to find the Key Fragment, even dismissing the child to just be eaten. Nevertheless, Compa explains to Neptune about the "NPC silhouette" that they have to rescue.
At the end of the cave, IF encounters a monster already dead. As she tries to identify the cause, a girl with white hair and wearing a black suit appears and explains that she already saved the child. The latter asks IF if a girl named Neptune is with her. Neptune arrives, and IF explains how the girl with white hair knows her and how they look like when Neptune transforms. Neptune says that she hasn't met the girl before. The girl then attacks Neptune with hostility.
The group routs the white-haired girl. IF asks if Neptune really did something to the white-haired girl, but Neptune explains that she doesn't remember doing anything to the white-haired girl. IF ponders if she made the right choice of siding with Neptune.
The group decides to find a heretic. IF explains how one is kicked out by the Basilicom for worshiping another goddess. The group wants to find information about the Basilicom from a heretic, expecting them to hold information for being former members. Neptune doubts that they'll never disclose any information, but IF suggests that they'll threaten them with Neptune's gun.
The group finds the heretic inside, who tells them to stay away. He also blurts out about how "the messenger" only knows the place. When Neptune asks about the Basilicom, the heretic opens up. He explains how the Parliament, "who only listens to coins", has more control than the Sanctuary, "who doesn't listen much either". IF explains how the Sanctuary evangelizes, while the Parliament governs. The heretic pronounces that humanity is doomed, making Compa wonder if the man is prophesying the apocalypse. The heretic replies that everyone will die by Overlord Momus's hands, a being powerful enough to seal away one of the goddesses. Neptune assumes that Momus is the cause of the monsters. When Compa doubts about if there's such a being like Momus, the heretic warns them about how Momus's messenger will punish them for killing the monsters. When dismissed harshly by the man, the girls leave.
As Neptune wonders about Overlord Momus, IF dismisses the heretic's spouting as nonsense. At Neptune's mention of rescuing Histoire, IF thinks that Histoire is "playing them" and the one that's creating the monsters and lure them. Suddenly, Histoire asks Neptune to explain that it's not true. She also warns Neptune that Arfoire, the one who sealed her will come for Neptune. Before Histoire could tell any more details, her voice disappears. IF assumes that Arfoire and Overlord Momus are connected to creating the monsters.
The trio arrive in Chevre's place to retrieve Chian's materials. Chevre reveals that Chian has been high-strung ever since she took over her after her father. Neptune presses the issue, making Compa think she's being rude, but Chevre discloses that Chian's father died due to a tragic accident. Chevre also tells the girls that he's known Chian since she was born due to his connections with her father. He also reveals that they had to abandon the place due to Avenir. Chian's mother also asked him to help, but he already committed to his shop. Neptune wants to stop Avenir, but Chevre replies that Avenir is under direct protection of Lastation's Parliament. Due to Avenir's large industry, they hold a majority of Lastation's residents possible to vote over the Parliament. IF decides to put some effort on the Avenir business.
Available after "Avenir and the Basilicom's Web 2" event
The group are assigned to save an Avenir employee. IF reveals that Avenir doesn't make weapons for human use. Despite Neptune's complaints, Compa presses the issue about how Neptune shouldn't be picky on who to save. After conversing, the trio heads on to save the Avenir employee.
The party finds the Avenir employee. The employee recognizes Compa and IF but doesn't recognize Neptune, who is in HDD form until she speaks up, surprising the employee. He tells them that he was attacked by monsters when prepping for the Tech Expo. Compa responds that the Tech Expo was cancelled, but the employee says that it'll still go as planned. The trio asks what Avenir will be showcasing for the Expo, but he keeps it a secret. Instead, he tells them that Avenir has been preparing for the Expo since Avenir's inception.
The group encounters the white-haired again, who wants to battle Neptune. Already transformed, Neptune asks why the girl is coming after her for clarification and apologizes for whatever she did to her. The white-haired girl reveals that the two are destined rivals but says no more unless Neptune prevails against her.
The white-haired girl is defeated again, but she says it's a draw and mentions that Lastation hasn't lost. Compa assumes that Lastation might be a huge transforming robot, but IF tells her that it might only be possible on Planeptune. Without saying anything, the girl retreats, and Neptune already reverted back on her human form before she could take chase.