蕾貝卡·布魯加甸造訪幾近荒漠的格蘭貝爾王國，遇見那裏的唯一一位人類居民四季，而對方想和她交朋友。

在前往布魯加甸途中，蕾貝卡鼓勵四季去申請冒險者卡，並要他擔任自己和哈比的保鑣。

知名B-CUBER拉碧麗雅説蕾貝卡的B-CUBE頻道很無聊，讓四季動怒。隨後，四季正式取得冒險者卡。

諾瑪行星上的時間是50年前，哈比和蕾貝卡在那裏遇到年輕的彗智博士，也就是很久以前曾救過哈比的人。

四季一行人為了救回琵諾，闖進希維爾的藏身處，但彗智卻趁着情勢混亂，打算自己帶走琵諾。

四季一行人正設法讓水之翼飛離諾瑪，彗智突然出現，他主動説要幫忙，但是提出了交換條件。

在海盜飛船骷髏妖精號上降落後，四季前往艦橋，要和艾爾熙·庫莉姆森正面對抗，打敗她並接收飛船。

女巫告訴四季伊甸星原現在由他主宰，還説這艘飛船尚未恢復真正的力量。

四季和其他人衝去救蕾貝卡，同時彗智和一個名叫焰的女人回到伊甸星原。

焰用她靈魂之刃的力量擊退修女的人馬。與此同時，蕾貝卡想出從依力嘉塔脱逃的計劃。

女巫和修女‧伊芙莉終於重逢，而焰説出了她來到伊甸星原上的真正動機。

大家在鐵之丘發現隱士後，推測她陷入了異常睡眠狀態，因為她的心已經壞掉。

大家進入虛擬行星迪基塔利斯尋找隱士。在被找到後，隱士卻執意不肯回到“伊甸星原”。

焰宣佈自己將投靠德拉肯喬。之後，另一個焰卻突然出現，讓西奇一行人震驚不已。

蜘蛛大爺入侵“伊甸星原”的系統，並開始從內部瓦解戰艦。只有隱士才能阻止他。

為了找到魔王四煌星之中的第四人，西奇一行人出發前往時之行星米爾迪安 。

在戰鬥競技場，小梅答應提供西奇一行人想要的信息，但前提是他們能擊敗各自的對手。

從小梅那裏獲得所需的信息後，“伊甸星原”啓航前往行星聖珠寶，讓焰與她的師傅重聚。

西奇和焰身陷勞動區，被迫為一位名叫紅女士的人物蒐集貴重金屬。

尼諾帶領麗貝卡、皮諾和哈比前往勞動區。幾人在那裏遇到名叫保羅的男子，他聲稱自己是武神的弟子。

年幼的焰曾身處戰火塗炭的行星。那時，武神為她提供了庇護，更親自撫養她。

西奇一行人與紅女士當面對質。焰見到了武神，不禁悲從中來。同時，德拉肯喬入侵紅眼。

有了瓦伊茲的軍火庫戰鬥服，擊敗巴克簡直易如反掌。在麗貝卡對抗尼諾時，西奇與紅女士操控的機械騎士對決。

在紅鐵騎和西奇之間的戰鬥結束後，西奇一行人返回“伊甸星原”。他們不得不跟大家宣佈一個壞消息。

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.