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 finding Hermit on Iron Hill, the crew deduces that she’s in an abnormal sleep mode as a result of her heart being broken.

The crew enters the virtual planet of Digitalis to search for Hermit, but when they find her, she stubbornly refuses to return to Edens Zero.

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

Spider hacks into Edens Zero’s system and starts to destroy the ship from the inside. The only one who can stop him is Hermit.

To find the fourth member of the Demon King’s Four Shining Stars, Shiki and the crew head for the Planet of Time, Mildian.

At Battle Coliseum, Xiaomei tells Shiki and the crew that she’ll give them the information they want — but only if they can defeat their opponents.

After obtaining the information they needed from Xiaomei, Edens Zero sets course for the planet of Sun Jewel to reunite Homura with her mentor.

Shiki and Homura find themselves in a labor zone where they’re forced to gather valuable metal for a figure known as Madame Kurenai.

Nino leads Rebecca, Pino and Happy to the labor zone where they meet a man named Paul, who tells them he’s Valkyrie’s disciple.

When Homura was a child on a war-torn planet, Valkyrie took her under her wing and raised her like her own.

Baku is easily defeated, thanks to Weisz’s Arsenal suit. While Shiki battles the Knight Gear controlled by Madame Kurenai, Rebecca fights Nino.

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.

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.

Shiki and the gang get through Dragonfall and arrive at the Aoi Cosmos, which is ruled by Poseidon Nero of the Oración Seis Galáctica, and land on a fire planet, Red Cave, at the suggestion of Witch. The planet is overflowing with Water Ether, and is an environment that is a far cry from a "fire planet" covered by the ocean. As the Edens Zero crew enjoy a brief vacation at the ocean, they discover a town beneath the waters...!

Within a temple adorned by reliefs of Mother, Shiki and the group meet Nadia, the temple's guardian. They hear from Nadia that the far end of the temple contains hints to finding Mother, but as they venture deep into the temple, they find a scorching cave…

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.

The robots attack the ship and Jin, Kleene and Laguna have to defend their new allies. Meanwhile, on the planet, Shiki and the others are confronted by Poseidon Nero, who has been ordered to eliminate all robots.

Shiki confronts Orc from Poseidon Nero's Commando Team "Beast". Orc tells Shiki that they were ordered by Nero and are on a mission to cleanse this planet, which was under the control of Ziggy.

The battle in Foresta continues its course. Rebecca tries to experiment a little more with the use of Cat Leaper, but Hermit meets someone from her past that causes her to relive certain traumas.

The battle in Foresta rages on and Elsie springs into action to help Shiki when Justice cuts his way.

The Doomsday System is activated and all of Foresta is in danger.

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.

Shiki and Laguna's former companions prepare to launch an attack on Nero and try to stop Orc from placing the bombs on the planet.