Hyperdimension Neptunia mk2 features a total of ten chapters, three of which can only be seen through special requirements.
The Hearts are fighting against CFW Magic, but she stands formidable against the CPUs, even stopping Neptune's weapon with her own hand. Nepgear is forced to watch as her sister and the other Hearts fall against their opponent.
Three years later, Compa and IF are sent on a rescue mission to liberate Nepgear and Hearts. With CFW Judge's overwhelming opposition and the Sharicite's lack of power, Compa and IF are forced to abandon the mission, managing to only rescue Nepgear in the process.
Nepgear finally awakens after days of sleeping. She tells IF, Compa, and Histoire about the events that transpired in the Gamindustri Graveyard three years ago. They are shocked to hear that CPUs were defeated so easily by one person and explain how ASIC's influence has grown over the years.
Histoire proposes that Nepgear goes out and obtain the aid of the Mascot Characters and CPU Candidates. The party rehabilitates Nepgear and regains shares for Planeptune before heading to Virtua Forest Depths in search of the mascot character. They are faced with Underling and IF force starts Nepgear's HDD with a kiss which allows her to take Underling down easily.
Upon winning, Underling still manages to destroy the Mascot Character and runs. The Mascot Character gives Nepgear the remainder of her power and then disappears. After this, the party returns to Planeptune to report their success to Histoire.
Nepgear and her party head to Lastation to obtain information on the Lastation Mascot Character, they meet Uni who refuses to help after finding out that Nepgear returned and not her sister, Noire. In order to find the location of the Mascot Character, the Oracle, Jinguji Kei, requires them to find materials for a device they're building. When they do that, they go and ask the Mascot Character for help. While she initially refuses she gives in when she realizes that just defending isn't enough and separates a part of power from herself to help Nepgear save the CPUs.
In Lowee they meet Rom and Ram after trying to save Rom who had been held hostage by Underling. This meeting resulted in a fight between the three CPU Candidates. They head to the Basilicom to meet with the Oracle Mina Nishizawa who refuses to give them information regarding the Mascot Character due to it being on a mission of national importance. Nepgear and party continue their search and eventually learn of its location by spying on Underling around Lowee. When meeting with the Mascot Character, she also refuses her help due to having to keep the Killachines sealed and also due to a promise she made to Neptune. Underling destroys the Mascot Character which causes the seal on the Killachines to be lifted. They meet Gust who can repair broken Mascot Character discs and gather the necessary materials for her to fix it. After doing this they manage to seal the Killachines once again with Rom and Ram's help and even manage to gain the help of the mascot disc due to it having split into two separate discs.
They head to Leanbox via Terraportation through Lastation after finally repairing one of the ships and learn that the Oracle Chika Hakozaki has lifted the ban on supporting Arfoire. They investigate the matter and learn that Underling has been pretending to be Chika while the real one was held hostage somewhere. They follow Underling all the way to the captured Chika who they take back to the Basilicom. Chika explains that ASIC has taken their Mascot Character hostage and so they all head back to where Chika was held hostage initially to reclaim it. With 5pb.'s assistance, they are able to defeat Underling and Pirachu and report back to Chika. Chika allows them to have the Mascot Character as long as they save Vert. Nepgear and the other candidates help Leanbox take shares from ASIC by performing at 5pb.'s concert. Once the concert is over, they all go their separate ways then 5pb. joins them on their journey to save the CPUs.
Histoire informs of ASIC attacking a nearby island in Planeptune territory and requests 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 its shares.
The party immediately heads to Lowee where they meet with Mina who is hesitant to let them help due to it possibly affecting Lowee's political standing. Nepgear offers a trade-off saying that in exchange for helping them she wants Rom and Ram to help her. Ram agrees to this and before Mina can object, Nepgear leaves. They learn that Pirachu's distribution of Arfoire Emulator Chips is the cause to ASIC's increase in shares and deal with him swiftly. They return to Lowee and make a miniature Sharicite for Rom only to find out she's been brainwashed and kidnapped by Underling and CFW Trick. They use Rom to attack Lowee but Nepgear and the others intervene by attempting to use the Sharicite to save Rom. It almost works but Underling takes her away and so the group follows.
After cornering Underling, Rom and Ram both accidentally end up brainwashed which results in the party having to fight both of them. They then use the Sharicite for a second time and this time manage to successfully save the twins. CFW Trick appears and is also defeated by the group before they return to the Lowee Basilicom. 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.
As they arrive in Lastation they are greeted by the young soldier who gave them information regarding the Hematite. He tells them 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 ASIC's leaders. They take her back to town only for her to go missing for a second time. Nepgear finds Uni at 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.
Nepgear, having now gained the aid of each of the Mascot Characters as well as the other CPU Candidates, heads back to Planeptune. There they have a meeting with the Oracles of each nation to discuss what their next course of action will be. Histoire explains that Kei had been working on a device that strengthens the power of the Sharicite which will help ensure that they are able to save the CPUs.
Histoire sends them to the Gamindustri Graveyard herself. When they arrive they head for where they say the CPUs last and ultimately come back into contact with CFW Judge. Nepgear starts to doubt her ability to fight against him and win due to having being defeated by him the first time. Uni and the others pep her by saying that she isn't alone anymore and that she has all of her friends to support her now so they will definitely win. The faith of her allies awakened a new power inside of her and bestowed upon her the Lilac mk2 processor set.
After the battle against CFW Judge and managing to destroy him, they use the Sharicite to restore power to the CPUs. This is then followed by a heartwarming reunion between the Candidates and their older sisters (though Vert felt left out due to not having a sister). Now having completed their mission the group returns to the Planeptune Basilicom.
With the CPUs now rescued, the Oracles and CPU Candidates discuss their next course of action. A large tremor from the Gamindustri Graveyard interrupts their discussion so Nepgear and the others go to check it out. Upon arriving they are met with a giant Pirachu who has become the vessel to a fragment of Arfoire's power. When they try to take action in defeating it, they are stopped and easily defeated by CFW Magic. Just as she is about to deliver the finishing blow, Nepgear and the others are saved by the CPUs. CFW Magic spares them saying her job is not to kill the CPUs and takes her leave. After this, the party goes to deal with the giant Pirachu in Gapain Field where they make quick work of him and cause him to revert back to his normal state.
The party returns to the Planeptune Basilicom where the Oracles tell them of their Sting Operation plan to embargo all of Arfoire's products. Nepgear and the others are requested to go out and fight any monsters unleashed by ASIC as well as to defeat the Four Felons to gain the support of their people. In the midst of doing this, they receive word of a factory developing Arfoire products and move in to take out and ultimately stop the production cycle. They fight Underling, who is in charge of the operation as well as CFW Brave. Upon winning against CFW Brave asks Uni if their path will truly lead the children to happiness. Uni promises that they can do it and will make sure they're always having fun. After asking for her name, CFW Brave entrusts his “flames of passion” to her and disappears.
With the factory now destroyed, Nepgear and the others are left with nothing to do until Vert receives a call from Chika telling her that Leanbox is under attack. The party makes their way to the scene with haste only to see Underling yet again as the source of the undergoing turmoil. The party easily deals with her and she flees right after. Chika calls Vert for a second time, informing them that the anarchy in Leanbox was a decoy and that Planeptune has fallen into ASIC's hands. The group heads to the Leanbox Basilicom where Chika informs them that ASIC wishes to tradeoff the CPU Candidates for Histoire at LAN Castle. While it is obviously a trap Nepgear, wanting to save Histoire, willingly goes along with the other Candidates.
When the Candidates arrive they are met with CFW Trick and Underling. They are forced to allow the two to do as the please to them otherwise, Histoire will be hurt. CFW Trick tries to convince the twins to join ASIC but Rom and Ram refuse, not liking the fact they can't protect their friends. They strengthen their resolve and power up. The CPUs and Makers arrive, having successfully taken Histoire back in while CFW Trick was distracted and immediately take him down.
The party returns to the Planeptune Basilicom and Histoire requests the aid of the other nations to reclaim Planeptune and for Nepgear and the others to deal with CFW Magic. Once they win, CFW Magic reveals that in the wake of her defeat that Arfoire will revive due to the Four Felons merely being vessels of a portion of Arfoire's power. As CFW Magic disappears, Arfoire revives.
The party returns to the Planeptune Basilicom and Histoire requests the aid of the other nations to reclaim Planeptune and for Nepgear and the others to deal with CFW Magic. Once they win, CFW Magic reveals that in the wake of her defeat that Arfoire will revive due to the Four Felons merely being vessels of a portion of Arfoire's power. She then adds to this by saying that since they struggled so much against one of the Four Felons that Gamindustri is most certainly doomed. As CFW Magic disappears, Arfoire revives.
The party returns to the Planeptune Basilicom to discuss their next course of action. Having struggled so hard against CFW Magic, they begin to doubt their ability to beat Arfoire on their own power. Nepgear suddenly remembers the story she heard about the unused cursed sword that can only be used to defeat evil. Having no other possibilities for defeating Arfoire, the Oracle begin doing research on the sword while Nepgear and the others go around and ask the townspeople for information.
They found out the location of the sword which is located in a secret passage in LAN Castle. They find the old rusty sword and try to restore it but to no avail. Histoire calls Nepgear and frantically requests for everyone to return to the Basilicom. There, the Oracles explain the legend surrounding the sword. In order for the sword to be used it must receive the offering of a CPUs life. The more CPUs it's given, the stronger it grows. Everyone is surprised and naturally refuses to use such a horrible method to defeat the Deity of Sin. Nepgear proposes that other nations pour their shares into Planeptune and allow Neptune and Nepgear to fight Arfoire; that way no one will have to die. The CPUs instantly decline, not wanting to sacrifice their nations before themselves.
Nepgear still decides to follow through with her plan and goes as far as taking the other nation's shares. In Lastation they are confronted by Noire and Uni due to taking their shares. Nepgear and Neptune are forced to fight against them and eventually Noire impales herself with the cursed sword, knowing there is no other way to save Gamindustri and because she is well aware that Neptune and Nepgear are stronger than she is. Uni follows suit, allowing Nepgear to impale her with the sword as well. In Lowee, they are confronted by Blanc, Rom, and Ram who also suffer the same fate after the fight for control of the sword. When they arrive in Leanbox they fight Vert who refuses to go down easily and causes them to retreat. Underling takes this a chance to attack Vert who is severely weakened. Nepgear and Neptune return to the scene after hearing her scream and see that she is on the verge of death after her run in with Underling. Nepgear, severely displeased, strikes down Underling and ultimately kills her. Vert, who is now on her deathbed, requests for them to finish her off with the sword due to her already being in the process of dying. Neptune complies and takes the sword from Nepgear to sacrifice Vert to the sword.
Having sacrificed all of the other CPUs, Neptune and Nepgear return to Planeptune. Neptune tells the others that she has a plan and takes Nepgear to the place they used to play at as children. Neptune suddenly asks Nepgear to kill her with the sword which Nepgear automatically refuses. Neptune tells her that it's all or nothing and can't afford to risk it not being enough when they face Arfoire. Nepgear eventually succumbs to Neptune's demands and impales her with the sword, breaking down into tears after.
The following day, Nepgear and the Makers head to the Gamindustri Graveyard for the final battle against Arfoire. When fighting, Arfoire allows Nepgear to strike her down with the sword, saying that she is only prolonging Gamindustri's inevitable doom. She goes on to say that eventually she will be summoned again and she will destroy the world. With those words, Arfoire vanishes. With Gamindustri saved, Nepgear becomes the world's only CPU and dissolves all the nations into Planeptune. She is constantly haunted by Arfoire's words and says she will prevent her revival by any means necessary.
Nepgear and the party return to the Planeptune Basilicom to discuss their next course of action. With the Arfoire now revived, their options are limited to heading to the Gamindustri Graveyard and fighting her head on. While Histoire is initially reluctant to follow through with this plan, she too accepts the fact that there is nothing left for them to do and allows them to proceed to the industry graveyard to fight against Arfoire, wishing them luck.
Normal/Branch End Route
The party arrives in the Gamindustri Graveyard and sees the incompletely revived Arfoire in her new vessel, the party readies themselves for the final showdown and proceeds in taking her on. After beating her vessels begin to collapse but it is soon revealed that she is not truly defeated. Vert deduces that unless they seal her away, that their victory will be a loss and so the four CPUs come together and use their bodies to seal Arfoire away for good.
Due to not coming back immediately, it is deduced that the CPUs are no longer alive which results in an inauguration ceremony for the CPU Candidates to become fully fledged CPUs. In the midst of it, the CPUs unexpectedly return just in time and are greeted warmly by their sisters.
The party arrives in the Gamindustri Graveyard and sees the incompletely revived Arfoire in her new vessel, the party readies themselves for the final showdown and proceeds in taking her on. After beating her, her vessels begin to collapse but it is soon revealed that she is not truly defeated. Arfoire makes preparations to move to another vessel and Vert deduces that unless they stop her core they will be unable to defeat Arfoire. Nisa and Neptune try to fight Arfoire again only to see that their attacks go right through her. Arfoire begins to merge with the Gamindustri Graveyard which calls for the party to retreat and think of another countermeasure.
The group returns to the Planeptune Basilicom to explain the situation to Histoire and the other oracles. Suddenly IF, Kei, Chika, and Mina all receive calls indicating that a member of the Four Felons is present in each nation. The Four Felons demand that everyone in Gamindustri worships Arfoire within ten days and if even one person refuses they will be killed. Mina remembers an old record of a war between a Planeptune CPU named Caelus and the Deity of Sin. While her body may no longer remain, Noire says that her soul may still be around. With the idea to ask Caelus for help, the party begins to search Planeptune which takes them to LAN Castle Secret Hall.
When they arrive, they noisily call out to her which causes the CPU to awaken. Under the impression that she had defeated Arfoire in the past, they ask for her help. Caelus explains that she had the aid of three other CPUs who had perished in the battle and that they were unable to defeat Arfoire. They were instead able to weaken her so that they could seal her away. Caelus explains that in order to physically harm Arfoire they must strike her with a will that is stronger than the evil one she is comprised of. Having gotten the information they required, the party heads back to the Planeptune Basilicom to report their findings. With only a day left to deal with the looming threat of The Four Felons, Histoire organizes a hot spring for them to relax before going off to fight.
The following day, the party heads out to each of the nations to deal with the Four Felons for a second time before returning to the Basilicom and discussing their next move which is to defeat Arfoire. They decide to head out in the morning and spend the night playing games to tire themselves to sleep. The CPUs end up arguing about who has the better console while the CPU Candidates just play on their handhelds and talk about which games they're playing. In the meantime, Histoire spends her time with the Mascot Characters.
As the party enters the Graveyard's heart they are confronted by Underling who intends to fight them one last time to avenge CFW Magic. While the others don't want to waste time on her, Nepgear respects her wishes and accepts her challenge. Pirachu fights alongside Underling, saying that she is his partner now and forever. Naturally, Nepgear and the others defeat the two and tell them to leave while they still can before making their way to Arfoire for the final battle.
When they make it to Arfoire, she is seen in her new vessel which is smaller than the last. After an exchange of words, Nepgear and the others face off against DOS Arfoire and successfully destroy her vessel. The graveyard begins to collapse and Arfoire states that she will find a new vessel. Not wanting to miss this chance, everyone pours their faith into Nepgear to combine their wills into one unified force. Nepgear takes down Arfoire with the power of everyone's faith and the Gamindustri Graveyard begins to fully collapse. The party makes a run for it and returns back to Gamindustri. After this, Nepgear narrates what happened three months after the defeat of the Deity of Sin.