Rebecca Bluegarden fa visita al Regno di Granbell ormai quasi deserto. Là incontra l'unico abitante umano, Shiki, che vuole esserle amico.

Rebecca incoraggia Shiki a registrarsi come avventuriero mentre si dirigono a Blue Garden, ma gli chiede anche di diventare guardia del corpo per lei e Happy.

Quando la famosa B-Cuber Labilia deride il canale B-Cube di Rebecca, considerandolo inferiore, Shiki perde la calma, poi ottiene la registrazione come avventuriero.

Sul pianeta Norma il tempo è 50 anni nel passato e Happy e Rebecca incontrano un giovane Professor Weisz Steiner, lo stesso che anni prima aveva salvato la vita a Happy.

Shiki e la banda si intrufolano nel nascondiglio di Sibir per riprendersi Pino, ma Weisz approfitta del caos e cerca di tenere Pino per sé.

Mentre Shiki e i suoi faticano a far decollare Aqua Wing da Norma, Weisz si materializza davanti a loro offrendo aiuto... ma in cambio vuole qualcosa.

Shiki sale sulla nave pirata Skull Fairy e si dirige subito sul ponte per affrontare Elsie Crimson in battaglia e conquistare il vascello.

Witch informa Shiki che ora è lui il possessore della Edens Zero, poi gli spiega che la nave non è ancora ritornata alla piena potenza.

Mentre Shiki e gli altri si precipitano a salvare Rebecca, Weisz torna sulla Edens Zero assieme a una donna di nome Homura.

Homura usa i suoi poteri Soul Blade per respingere gli uomini di Sister. Nel frattempo Rebecca pianifica la fuga dalla Illega Tower.

Il Cronofago si avvicina inesorabilmente al pianeta Guilst e Shiki è disgustato nel vedere che Sister usa Jinn come scudo. Poi improvvisamente appare un'altra Sister!

Witch e Sister Ivry sono finalmente riunite e Homura rivela la vera motivazione che l'ha spinta a venire a bordo della Edens Zero.

Dopo aver trovato Hermit sulla collina, la squadra deduce che si trova in uno stato di standby anormale a causa del suo cuore spezzato.

La squadra entra nel pianeta virtuale di Digitalis in cerca di Hermit, ma quando la trovano lei rifiuta categoricamente di tornare sull'Edens Zero.

Homura dichiara di volersi unire alla banda di Drakken Joe, ma Shiki e gli altri rimangono sconvolti quando si trovano davanti un'altra Homura.

Spider si infiltra nel sistema dell'Edens Zero e inizia a distruggere la navicella dall'interno. Solo Hermit è in grado di fermarlo.

Per trovare la quarta stella luminosa del Re Demone, Shiki e compagni si dirigono sul pianeta del tempo, Mildian.

Al Battle Colosseum, Xiaomei dice a Shiki e alla squadra che darà loro le informazioni che vogliono a patto che sconfiggano gli avversari.

Dopo aver ottenuto le informazioni di cui avevano bisogno da Xiaomei, l'Edens Zero fa rotta verso il pianeta Sun Jewel per riunire Homura con la sua maestra.

Shiki e Homura si ritrovano nei campi di lavoro dove devono raccogliere preziose unità metal per la misteriosa Madame Kurenai.

Nino conduce Rebecca, Pino e Happy nei campi di lavoro dove incontrano un uomo di nome Paul che afferma di essere un discepolo di Valkyrie.

Homura è una bambina in un pianeta devastato dalla guerra quando Valkyrie la prende sotto la sua ala protettrice allevandola come una figlia.

Shiki e gli altri affrontano Madame Kurenai. Alla vista di Valkyrie, Homura è sopraffatta dalla tristezza, mentre Drakken Joe si infiltra nell'Occhio Cremisi.

Baku è sconfitto senza difficoltà, grazie all'arma Arsenal di Weisz. Mentre Shiki combatte contro il Knight Gear di Madame Kurenai, Rebecca lotta con Nino.

Alla fine della battaglia tra il Dragone Kurenai e Shiki, questa torna con i suoi sull'Edens Zero per condividere le brutte notizie con il resto della squadra.

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.

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.