Rebecca Bluegarden visits the nearly deserted Granbell Kingdom. There she meets the sole human inhabitant, Shiki, who wants to be her friend.

Shiki loses his cool when famous B-Cuber Labilia makes fun of Rebecca’s inferior B-Cube channel. Then, Shiki gets his official adventure license.

On the planet Norma, where time is 50 years in the past, Happy and Rebecca meet a young Professor Weisz, who long ago saved Happy’s life.

Shiki and the gang break into Sibir’s hideout to get Pino back, but Weisz takes advantage of the chaos to try and take Pino for himself.

After boarding the pirate ship Skull Fairy, Shiki makes his way to the bridge to confront Elsie Crimson and fight her for the vessel.

After Homura declares that she’s joining Drakken Joe, Shiki and the crew are shocked when another Homura suddenly appears.

After the battle between the Kurenai Dragoon and Shiki comes to an end, Shiki and the others return to the Edens Zero and have to share some bad news.

"You've lived enough, time to sleep," says Shiki, who has reached Overdrive and defeated Drakken Joe. However, Weisz's anger does not subside, and he stands over and points his gun at the barely alive Drakken Joe.

Before they venture beyond the cosmos in search of Mother, the Goddess of the Cosmos, Edens Zero visits Granbell at the request of Shiki, where he has an unexpected reunion.

Edens Zero is cornered by Edens One and Shiki and the crew are saved at the nick of time by the space pirate Elsie Crimson. After the battle, Elsie boards Edens Zero and talks to Shiki about something Ziggy had asked her to do a long time ago.

With Laguna's help, Shiki and the gang obtain a hint for finding Mother and leave Red Cave towards the Verdant Planet Foresta. Meanwhile, Elsie's pirate gang, cruising through the Aoi Cosmos on the Skull Fairy, are being pursued by Justice of the Cosmic Government's Interstellar Union Army.

Now that everyone's back on the ship, Shiki introduces Xenolith, who has some disturbing statements that affect Shiki and his companions. Meanwhile, Oceans 6, Poseidon Nero's group, assembles and prepares for their next move.

Under Xenolith's guidance, Shiki and his friends receive VR "bondage training" to overcome decline of Ether levels when they are constrained. During this training, Ziggy suddenly appears and hurts Rebecca with gravity, infuriating Shiki and causing him to break out of his constraints.

After Poseidon Shura's "Judgment Day" declaration, Shiki and his friends decide to think of a way to counterattack. Laguna suggests an idea that will take Edens Zero to the desert of Planet Sandra.