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

On their way to Blue Garden, Rebecca encourages Shiki to get his adventure license. She also asks him to be a bodyguard for her and Happy.

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.

While Shiki and the gang struggle to fly Aqua Wing off of Norma, Weisz suddenly appears and offers to help — but he wants something in return.

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

Witch informs Shiki that he is now the master of the Edens Zero. She further explains that the ship has not yet returned to its full power.

While Shiki and the others rush to rescue Rebecca, Weisz returns to Edens Zero along with a woman named Homura.

Homura uses her Soul Blade powers to fight off Sister's men. Meanwhile, Rebecca plans her escape from Illega Tower.

As the chronophage moves ever closer to Planet Guilst, Shiki is disgusted to see Sister use Jinn as a shield. Then, another Sister appears!

Witch and Sister Ivry finally reunite, and Homura reveals her true motivations for coming aboard Edens Zero.

After defeating Madame Kurenai and leaving the planet Sun Jewel, Shiki and his comrades continue their journey and attempt to infiltrate Belial Gore, the enormous urban-type battleship of Drakken Joe, who has been targeting Edens Zero.

Shiki and his gang believe they have successfully infiltrated Belial Gore, but Drakken Joe had been aware of their every move and sends out his elite military force, the Element 4, to take down Shiki's group.

Within the Belial Gore, Weisz dons an Arsenal suit in his fight against the Element 4 Spirit of Water, Laguna. However, he finds it difficult to gain the upper hand due to Laguna's various water attacks.

Although Rebecca and Happy go into Belial Gore to deliver medicine to the injured Weisz, they are found by the Sylph of the Wind and captured. Shiki, Homura, and Pino receive Rebecca's communications and go to the loading docks, only to find that Rebecca is not there and in her place is the Element 4 Sylph and another "surprising" individual.

Although Shiki and Homura want to deliver medicine to Weisz as soon as possible, they struggle with the attacks from Sylph of the Wind and his assistant, Jinn.

Rebecca is devastated by Shiki's death and Drakken Joe finally explains to her in detail what it is he wants to extract from her. Apparently, she has a very particular Ether Gear.

As her Ether Gear powers are activated, Rebecca goes back in time to before the Belial Gore infiltration and offers information to Shiki. Master Noah appears in front of Shiki and the gang, as they arrive at Drakken's hideout and says that he has a message for Rebecca.

Changing into her Battle Dress, Hermit fights off the Element 4 sniper, Fie. Sister fights Daichi of Earth, Homura battles Sylph of Wind, and Witch stands against Laguna of Water. Meanwhile, Shiki and his gang push forward toward Drakken's hideout.

Shiki and the gang grasp a secret clue about Drakken Joe. As they discuss strategies for their next course of action, they notice that something is wrong with Labilia… Suddenly, Drakken Joe appears, sensing an Ether reaction. A head-to-head battle between Shiki and Drakken finally begins!

The fierce battle between Shiki and Drakken continues. Drakken activates his Overdrive to overwhelm Shiki, but suddenly Arsenal appears!

"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.