The fierce battle between the Kurenai Dragoon, which has released its true powers and Shiki come to an end. Homura faces Madame Kurenai and says that she needed someone to "love", even if it was a machine. Shiki and his group return to Edens Zero to face the reality of the "death" of a dear friend with a heart.

Weisz defeats another member of the Zaiten Three, Fuzaiten Baku (Ax of Heaven) using a new power--the Arsenal. Meanwhile, a heated battle with Madame Kurenai's Knight Gear "Kurenai Dragoon" continues. Kenzaiten Nino, Fist of Heaven, stands in the way of the Resistance and Rebecca's group. They find that guns are useless against Nino, who uses the Ether Gear 'Soul Arm', but Rebecca feels something strange happening to her leg. Ether from her entire body gathers into her leg to activate her Ether Gear!

Shiki barges in to Madame Kurenai, who had activated "Satellite Blaze" to destroy the labor district. He defeats the "Emissaries of Damnation" one by one, and goes forward angrily. Meanwhile, Homura is overwhelmed by sadness in front of Valkyrie's corpse. Rebecca tells Homura that Valkyrie knows how she feels. At the same time, Drakken Joe hacks into the "Satellite Blaze" and controls it. With full-fledged war on the horizon, Madame Kurenai orders to activate the "Kurenai Dragoon".

Homura was taken under Valkyrie's wing when she was young and living on her war-torn home planet. Although people tend to say that "robots cannot replace a real mother", Homura truly respected the strong and kind master Valkyrie. However, Valkyrie felt that "Homura needs a human mother" and leaves to find her. The "truth" of what happened to Valkyrie, who had never returned, was a harrowing one for Homura.

Rebecca and her friends go toward the hatch connecting the labor district under the guidance of Nino. She finds out that Nino is called 'Kenzaiten Nino, Fist of Heaven' and works for Madame Kurenai, who is searching for Edens Zero. Rebecca's group enter the labor district and meet Paul, who says he is a "disciple of Valkyrie". Meanwhile, Shiki has defeated 'Benzaiten Garrot, Scourge of Heaven', and Garrot activates the "Satellite Blaze", causing Shiki and Homura to be sent to Black Rock, the home of the mine master.

Shiki and Homura are sent to the labor district from the Gold Palace, where the wealthy citizens of Sun Jewel live. They are collared and forced to excavate resources according to the displayed number. To make matters worse, these metal resources can only be obtained by killing living minerals called "Stones". Who is making them do these terrible things? The workers say that it is "Madame Kurenai", the most powerful being on the planet...!

Edens Zero sets its course with the information that "Valkyrie is on Sun Jewel" from Xiaomei, On their way there, in the outer cosmos "Aoi Cosmos", they come across a school of fish. They find a man in a space suit stranded within the fish and rescue him. The man's name is Captain Connor, whose ship was in an accident causing him to become lost. He thanks them for their help and offers to "be the captain of this ship".

Shiki and his friends are guided towards the battle coliseum by Xiaomei, who lives on the planet Mildian. Shiki's group has to fight warriors sent in by Xiaomei in exchange for information on Valkyrie. Shiki, Rebecca, and Weisz struggle but ultimately triumph over the challengers sent by Xiaomei, and Homura prepares to fight the last challenger. However, when she sees the last fighter, Homura is rendered speechless...!

Hermit returns to the Edens Zero, bringing the count of the "Four Shining Stars" to three. Shiki and his friends go to "Mildian the Planet of Time" in search of the "Legendary Fortuneteller of the Sakura Cosmos" in hopes of finding Valkyrie. Meanwhile, Drakken Joe learns about Edens Zero from Spider. "This smells like money"...a message from a surprising individual is received....!

Edens Zero, hacked by Spider, who finally shows his true colors, starts to collapse from the inside. Only Hermit can bring the system back to normal. However, Hermit refuses to come out of the dress factory and help. "I don't care anymore..." says Hermit while reminiscing on her past, when she dreamed of "friendship between machine and men" and a cruel betrayal that happened 15 years ago.

Homura turns her back on the crew, saying she will "join Drakken Joe". Shiki and his friends are shocked. However, another girl who claims to be Homura appears and confuses them. Homura says that she was captured upon her arrival in Digitalis, and seeks the escaped fake Homura. As Shiki's gang struggle with the cheating Jamilov, the shut-off Hermit advises them to "cheat as well".

Shiki's group finally find Hermit on the Super Virtual Planet Digitalis, but Hermit stubbornly refuses to return to the Edens Zero with them. Shiki and his friends are perplexed when Hermit voices her hate for humans. What happened to her? Meanwhile, a player, Jamilov, has been continuing to do evil deeds within Digitalis. He sends out a swarm of monsters to attack the town of Crysta...!

Hermit, one of the "Demon Kings's Four Shining Stars" is found in an abnormal sleep state on Blue Garden's Iron Hill. She was in condition in which her "heart" was damaged and her soul is in a deep dive state within the digital world of 'Super Virtual Planet Digitalis'. Upon discovering this, Shiki and his friends digitalize themselves and dive into Digitalis...!

Shiki and friends beat Rogue Out and the fake Sister, and saves Rebecca and the B-Cubers from Illega's clutches. They barely make it out of planet Guilst just before it is swallowed by the "Chronophage". Witch and Sister have a happy reunion within the ship. Homura, who helped rescue Rebecca, finally discloses her true reasons for boarding the Edens Zero...

The "Chronophage" approaches the planet Guilst threatening the sheer existence of Shiki and his friends if they are swallowed by it. With only 60 minutes until its arrival, Happy and Witch panic. Meanwhile, a heated battle continues with a Rogue Out boy, Jinn, who uses an Ether similar to Shiki's. Sister joins the battle and has no qualms about using Jinn as a shield. Shiki is angered by the way Sister fights, but another "Sister" appears in front of them!

"Sister" appears before Shiki, Weisz, and Homura. Shiki attempts to admonish her misdoings as a member of the "Four Shining Stars", but Sister ignores him and sends her men to attack. Homura activates her Ether Gear "Soul Blade" to face the attack. Meanwhile, Rebecca and the other captured B-Cubers attempt to escape the Illega Tower.

Rebecca and other B-Cubers are taken prisoners by the mercenary gang Rogue Out, and discover that their boss is called "Sister". Meanwhile, Edens Zero dashes to save Rebecca, while Weisz comes back to the ship with a girl named Homura, who asks to board Edens Zero in exchange for rescuing Rebecca. With Homura, who uses Ether Gear, Shiki's group ventures on to the planet Guilst, known as a villains' den.

The space battleship "Edens Zero" finally shows its true form. Witch, one of the "Demon King's Four Shining Stars", says that the Edens Zero is the legacy of Ziggy, Shiki's foster guardian, and that Shiki should be the master of the ship as the next Demon King. She also says that all of the "Demon King's Four Shining Stars" need to be present so that Edens Zero can unleash its true power. Shiki's group visit Blue Garden once more in search of one of the Four Shining Stars, Sister.

Shiki and friends are captured on the space pirate Elsie's ship, the Skull Fairy. They fight creepy enemies in their attempt to capture this large ship, and reach the bridge where Elsie awaits. A fight between a skull-headed Elsie, who had been waiting for the "one inheriting the power of the Demon King" and Shiki ensues.
At the same time, the Interstellar Union Army's Justice and his fleet were closing in on the Skull Fairy and Elsie!

Although Shiki's group was able to rescue Pino, they uncover puzzling information stating that the last person to conduct maintenance on Pino was Professor Weisz. As Weisz struggles to get away from the police and leave planet Norma, he boards the Aqua Wing. He asks to let him have the ship, his arm starts to shine with Ether Gear!

Pino returns to Sibir, and is about to suffer the "consequences of leaving Sibir" before Weisz comes to save her just in time. Shiki's group also arrives at Sibir's hideout to save Pino. While Weisz attempts to take Pino and leave during this commotion, an enormous Knight Gear appears and a heated battle breaks out with Sibir's gang!

Shiki's group arrive at planet Norma, where time has gone back 50 years for some reason. They meet the younger counterpart of Professor Weisz, who saved Happy in the past. Naturally, Weisz has no recollection of Rebecca or Happy, and the group, who wanted Weisz to provide them with a spaceship, is let down. What is more, Weisz is being chased by the outlaw Sibir family!

The popular B-Cuber Labilia appears in front of Shiki and Rebecca, who have been able to rescue Happy. Labilia taunts Rebecca for having fewer channel subscribers, causing Shiki to make a scene for "making his friend cry". The space pirate Elsie and her gang also arrive looking for Shiki, causing a commotion on Blue Garden.

Shiki leaves his planet with Rebecca and Happy and arrives at the planet Blue Garden, where adventurers gather. The group visits the Shooting Starlight adventurers' guild, where Shiki is mesmerized by the hologram of "Mother", a mysterious lifeforce existing somewhere in the universe. She is worshipped as a "deity that will fulfill wishes "but Shiki has a feeling that they have met before. It is then when outlaws kidnap Happy!

The kingdom of Granbell is a robot theme park, where everything is a machine! Rebecca and her buddy Happy are the first visitors in 100 years. They meet a human boy, Shiki, and are initially baffled by his interest in other "humans", but hit it off in time. However, that night, something odd happens to the machines in Granbell...!

"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. Shiki's gang rushes to the scene, and Shiki cries at the sight of them unharmed. After this, Weisz comes to terms with his past with Sibir. Edens Zero departs to the planet Blue Garden, where Master Noah is.

The fierce battle between Shiki and Drakken continues. Drakken activates his Overdrive to overwhelm Shiki, but suddenly Arsenal appears! Weisz, who now knows the truth about the life support system, furiously attacks Drakken. Meanwhile, with the help of Jinn, Hermit successfully hacks the life support system. They are able to reverse the energy flow of Drakken, however...

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…Her true identity was a person only known to Homura! It was then that suddenly, Drakken Joe appears, sensing an Ether reaction. A head-to-head battle between Shiki and Drakken finally begins!

Changing into her Battle Dress, Hermit beautifully 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. There, an old Sibir appears and talks about the past between Weisz and Sibir, and their relationship with Drakken Joe.

As her Ether Gear "Cat Leaper" powers are activated, Rebecca goes back in time to before the Belial Gore infiltration and offers information to Shiki, who decides to launch a head-on attack to Belial Gore! Once more, Demon King's Four Shining Stars including Homura face the Element 4. A four versus four battle erupts! Meanwhile, Master Noah appears in front of Shiki and the gang, as they arrive at Drakken's hideout. Master Noah says that he has a message for Rebecca.

The efforts of Shiki and his friends fail and they are all captured, with Shiki losing his life. In this hopeless situation, Rebecca is locked away from everybody else by Drakken Joe. This is the start of the world without Shiki. Rebecca takes a shower in her isolated room, attempting to get herself together and organize her thoughts. As Rebecca cannot help but become emotional and shed tears on how she misses everybody, her body starts to undergo a change...!

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. Jinn had become more powerful than the last time they met him on the planet of Guilst. Meanwhile, although Rebecca attempts to set Labilia free, one Element 4, Daichi of Earth, appears and captures Rebecca... During this, Shiki and Jinn continue to battle fiercely until a person appears in front of them...!

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. They wake up and find Drakken Joe in the room with them. 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.

Thanks to Witch, all intruders upon the Edens Zero were eliminated. Meanwhile, 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. Arsenal launches a counterattack with the advice of Hermit, but is faced with another member of the Element 4 creeping up on him.

Shiki and his gang believe they have successfully infiltrated Belial Gore, but Drakken Joe had been aware of their every move, and his minions invade Edens Zero instead…! On Edens Zero, Rebecca, Happy, Mosco, and three of the Four Shining Stars confront these intruders. Meanwhile, Drakken Joe sends out his elite military force, the Element 4, to take down Shiki's group. The gang faces up with one member of the Element 4...!

After defeating Madame Kurenai and leaving the planet Sun Jewel, Shiki and his comrades accept Valkyrie's death and continue their journey. Rebecca, elated because her Ether Gear "Leaper" powers have awakened, becomes slightly delirious after bathing in the Spa of Eden and sees a peculiar dream. While Rebecca is out cold, Shiki and his gang attempt to infiltrate Belial Gore, the enormous urban-type battleship of Drakken Joe, who has been targeting Edens Zero.