丽贝卡·蓝色花园走访几近荒芜的格兰贝尔王国，并遇到了王国内唯一的人类居住者西奇，后者想和她成为朋友。

在前往蓝色花园的路上，丽贝卡鼓励西奇取得自己的冒险者卡，并请他担任哈比和自己的保镖。

B-立方主拉比莉亚嘲笑丽贝卡的 B-立方频道不入流，致使西奇情绪失控。随后，西奇拿到了正式的冒险者卡。

在诺玛行星上，时间倒退至 50 年前，而哈比和丽贝卡在此遇到了年轻时的瓦伊兹博士，他曾在很久之前救过哈比的命。

为了抢回皮诺，西奇一行人闯入了西维尔的藏身之处。然而，瓦伊兹却想趁乱将皮诺占为己有。

西奇一行人在驾驶水翼离开诺玛行星时遭遇困难，瓦伊兹突然出现并伸出援手，可他也要求他们提供回报。

登上骷髅妖精号之后，西奇前去桥上对战艾露茜·克里莫森，想要从她手中夺取战舰。

女巫告知西奇他已成为“伊甸星原”的主人，但也提到该战舰尚未恢复其真正的力量。

当西奇一行人赶去营救丽贝卡时，瓦伊兹与一位名叫焰的女子一起回到了“伊甸星原”。

焰使用灵魂之刃击退修女的手下。与此同时，丽贝卡计划逃出伊力加塔。

噬时逐步逼近吉尔斯特行星，修女利用吉恩做自己的挡箭牌，这让西奇倍感厌恶。随后，另一个修女出现了！

女巫和修女伊芙瑞终于重聚。焰坦承自己登上“伊甸星原”的真实意图。

大家在铁之丘发现隐士后，推测她陷入了异常睡眠状态，因为她的心已经坏掉。

大家进入虚拟行星迪基塔利斯寻找隐士。在被找到后，隐士却执意不肯回到“伊甸星原”。

蜘蛛大爷入侵“伊甸星原”的系统，并开始从内部瓦解战舰。只有隐士才能阻止他。

为了找到魔王四煌星之中的第四人，西奇一行人出发前往时之行星米尔迪安 。

在战斗竞技场，小梅答应提供西奇一行人想要的信息，但前提是他们能击败各自的对手。

从小梅那里获得所需的信息后，“伊甸星原”启航前往行星圣珠宝，让焰与她的师傅重聚。

西奇和焰身陷劳动区，被迫为一位名叫红女士的人物搜集贵重金属。

尼诺带领丽贝卡、皮诺和哈比前往劳动区。几人在那里遇到名叫保罗的男子，他声称自己是武神的弟子。

年幼的焰曾身处战火涂炭的行星。那时，武神为她提供了庇护，更亲自抚养她。

西奇一行人与红女士当面对质。焰见到了武神，不禁悲从中来。同时，德拉肯乔入侵红眼。

有了瓦伊兹的军火库战斗服，击败巴克简直易如反掌。在丽贝卡对抗尼诺时，西奇与红女士操控的机械骑士对决。

在红铁骑和西奇之间的战斗结束后，西奇一行人返回“伊甸星原”。他们不得不跟大家宣布一个坏消息。

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.