Somewhere in a clearing in a forest, Nepgear and Neptune decides to make a decision to sacrifice the latter for power. By killing Neptune with the sword, Nepgear will have the power to stop a force coming from the sky. After slashing Neptune, Nepgear laments over killing her sister. Neptune's voice calls out her name. Looking below, Nepgear sees her sister in dogoo form and starts to multiply and overwhelm her.
In Nepgear's room, Compa, IF, Histoire, Neptune, and Vert checks up on a sleeping Nepgear. It seems that Nepgear has caught the Bad End Syndrome, which puts her in a state of fever and causes her to dream of "bad ends."
With all of the CPUs communicating via web chat, they discuss about how to return the sick CPU Candidates back to normal. Knowing a possible cure, Histoire talks about the Shimmering Flower, which can kill the syndrome fast, but it is rare in where they are. The only place where they could find them more easily is in the Ultra Dimension.
Neptune and Vert travels to the other dimension, but somehow they cannot transform, causing them to end up falling on the ground in a forest somewhere. The two end up meeting the dimensional counterparts of Blanc, Vert, and Noire. Plutia comes by moments later to greet them. While traveling back to Planeptune, the group talks to each other about various things.
Arriving in Planeptune's Basilicom, Neptune and Vert meets Histoire's counterpart, a smaller version of what they know. On the corner, Neptune sees Peashy and gestures her to come and greet her. Neptune ends up get tackled by Peashy, showing how Peashy thinks Neptune is still weak.
After a while, the group travels to the Cursed Hell Devil Death Bloody Spectral Tower, a gloomy tower surrounded by dark skies. With 10,000 floors and very powerful monsters, the Shimmering Flowers are supposedly at the top floor. Since the two Hyper Dimension CPUs can't transform in the Ultra Dimension, the others are coming with them. They're also imposed with a three-hour time limit before a gate back to their dimension opens, an occurrence that can only happen every three years.
With a new elevator built on the tower, the group manages to travel from 4th floor to the 9,999th floor in two hours. With powerful monsters, Blanc, Vert, Noire, and Plutia handles the monsters, while Neptune, the Vert of the Hyper Dimension, and Peashy warps to the top floor to gather the flowers. Powerful monsters also roam the top floor, so Peashy transforms to handle them. Overwhelmed, Peashy gets caught in a bind, so Neptune gives Vert the flowers to help. Vert is transported back by Plutia in Planeptune due to approaching time limit. Vert is beamed back to the Hyperdimension without Neptune.
Peashy wonders why Neptune stayed. She answers about how she got to fight alongside with her. The other three warps near Neptune's position and also wonders why Neptune stayed. For now, they decide to travel back to Planeptune's Basilicom. Trying to operate the warp point, rather than exiting the tower, she opens up a warp point to her original dimension, the exact point being in a cave where the Hyper Dimension's Noire and Blanc are trying to find Shimmering Flowers. Noire and Blanc meets their dimensional counterparts and talk to each other.
Thanks to Neptune, a permanent gate is opened between the Hyper Dimension and the Ultra Dimension. Nepgear chases Peashy around for her N-Gear, while Plutia shows Compa and IF a picture of their dimensional counterparts. At the end, Peashy presents and gives Neptune pudding that she baked.
At the credits, it's shown that the other Ultra Dimension CPUs traveled to the Hyper Dimension to mingle with their counterparts.
- The CPU Candidates became sick with the Bad End Syndrome.
- Neptune and Vert traveled to the Ultra Dimension to seek the Shimmering Flowers, a cure to the Bad End Syndrome.
- Neptune and Vert successfully gathered some Shimmering Flowers, but Vert was the only one who was able to travel back to the Hyper Dimension via the gate.
- Courtesy of Neptune, a permanent gate is opened between the Hyper Dimension and the Ultra Dimension.
Neptune and Vert end up traveling in the Ultra Dimension to find the Shimmering Flower. The CPUs of the Ultra Dimension help the two to retrieve some flowers in the Cursed Hell Devil Death Bloody Spectral Tower.
Characters are shown in order of appearance.
These characters are shown but only made a cameo appearance:
- Nepgear's dream is a reference to the Conquest Ending in Hyperdimension Neptunia mk2.
- When Yellow Heart rescues Neptune from the Ancient Dragon, it's a near shot-for-shot recreation of the scene from the first episode when Neptune rescued Noire from the same enemy.
- This episode marks the return of Plutia and Peashy respectively.
- The Cursed Hell Devil Death Bloody Spectral Tower is a reference to Idea Factory's video game Spectral Tower.
- This is the first and only episode where Neptune doesn't transform in her HDD form same with Noire, Blanc and Vert.
- However, the Ultradimension versions of Noire, Blanc and Vert do transform in the HDD forms.