[13] The game is separated into three individual chapters with different stories for each dimension, each with a unique title:[14] With the era of peace continuing throughout Gamindustri, Neptune, the ruling Console Patron Unit (CPU) and Nepgear, her sister and CPU Candidate of the nation of Planeptune are warned by their Oracle, Histoire, of the upcoming 'CPU Shift Period', where the public will attempt to oust their CPUs in favor of newcomers.

The pair learn that, like Uzume, they are unable to transform to unlock their true powers in this world due to the absence of Shares (faith from the people).

She is also an amnesiac who remembers nothing of her people or the calamity which destroyed her world but believes it to be the work of a giant known as Dark Purple.

Nepgear works on a device to send herself and Neptune home but the facility is attacked by Arfoire; a powerful CPU-like being with a lust for destruction.

Uzume and her friend Umio plan to rebuild their world, though the older Neptune's fate is left uncertain.

The three head to the Basilicom where Histoire welcomes them home and reveals that B-Sha from Gold Third is an even lazier leader than Neptune, and is also afraid of monsters.

In an effort to woo Compa, Warechu reveals the names of several AffimaX members, including himself, Arfoire, Steamax and their leader, the capitalist General Affimojas.

Later, the tower is attacked by The Order, hoping to cut off K-Sha's power source; the crystal on the top floor.

C-Sha claims she has no memory of their prior battle and tells Blanc about the harsh class system in Lowee and the restrictive laws.

Blanc joins C-Sha and becomes a hunter and helps the struggling citizens whilst searching the land for her sisters, Ram and Rom.

After reuniting with Rom and Ram on a rescue mission, Blanc is approached by Azna=Leb and tasked with investigating C-Sha following troubling allegations against her.

C-Sha is sentenced to execution but releases the mist, summoning an army of monsters to attack Lowee, allowing her to escape with help from her friend Financier.

After liberating Lowee, C-Sha reclaims her position of ruler and arrests Azna=Leb who she left in charge in her absence, and then abolishes the harsh laws and class system which he set in place.

S-Sha promises to return Leanbox to Vert after they defeat the demon king, but she disappears soon after the mission is accomplished.

After recruiting Nepgear, Vert, Noire, Uni, Blanc, Ram and Rom, the party return to Planeptune to plan their next move against AffimaX.

After sparring with Nepgear, Uni, Ram, Rom, Compa and IF, the four members of Gold Third agree to join the rescue mission.

Nepgear, Uni and Uzume leave the party to rest whilst they explore the area and rescue older Neptune from Arfoire, and destroy her once and for all.

Older Neptune reveals she was a double-agent who joined AffimaX to aid the party from the shadows by stopping S-Sha's ritual and leaving the doppelganger's portal open.

With older Neptune back in the party, the group explores Heart Dimension and learn that Kurome has the power to induce nightmares and false happiness, which she is using to corrupt the CPUs like she did previously to Affimojas and Gold Third.

She also partially re-wrote the timeline to make the public forget, and thus weaken, the CPUs, but newly acquired Shares are cancelling its effects.

The party track down Kurome, who reveals she is a spirit of the real Uzume; an old CPU of Planeptune who volunteered to be sealed in Heart Dimension by Histoire after unintentionally harming her people having failed to control her powers.

There, she came to resent humankind who shunned her and became a wandering spirit, whilst a fragment of her power; her conscience, took on a new life in the connected Zero Dimension, as the new Uzume.

Kurome reveals that Uzume's growing power also increases her own, allowing her to physically manifest in the Hyper Dimension, leaving the party to battle her latest giant, who they destroy, along with several CPU clones.

Uzume buys the party enough time to evacuate themselves and the friendly monsters, including Umio, back to Hyper Dimension.

[21] Compile Heart initially considered releasing each of the three chapters as separate games, and as a result different title logos were created for each story.

[9] The game is produced by Naoko Mizuno, alongside director Shingo Onodera and character artist Tsunako.

In addition to the story are the VR events that can be unlocked where the main four goddesses visit the player and spends time talking about themselves.

Another form of VR events happens during the main story as the adult version Neptune visits the player.

[30] Marcus Estrada of Hardcore Gamer gave the game a 3 out of 5 saying, "Megadimension Neptunia VII is slightly refreshing, but not enough to really revitalize this aging series.

"[31] CJ Andriessen from Destructoid rated the game a 6.5/10 saying, "Megadimension Neptunia VII opts not to use its transition to the new hardware as a reason to try and expand its audience beyond the current player base.