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From a confession made by Mid, grandson of the legendary and courageous Cid, the true identity of the plunderer of the Crystals is revealed. Prettz, Linaly, Rouge and Valkus have been asked by Queen Lenna to recover the Crystals of Earth, Water and Fire. With the help of the Flying Dragon, guardian god of Tycoon kingdom, they were determined to venture into the Evil headquarters: The Black Moon. But just as they were about to begin their journey, the enemy made a surprise attack and kidnapped Linaly in whose body the Crystal of Wind temporarily resides...
The chapter opens with Ra Devil stating how it has been so long since he took the brain of the great scientist Cid two hundred years ago, while said brain is shown. The picture then shifts to show Ra Devil himself who is in bad shape and only held up by a multitude of machines. He states that he has wandered the universe in search of the truth before finding it ultimately in Deathgyunos. He then closes his speech by saying that the time has finally come for him to become Deathgyunos himself, ruler of the universe.
He then shows us the four crystals that have been placed in a machine, where Linaly takes the place of the Wind Crystal due to carrying it inside her. Ra Devil and his Deathgyunos soldiers then start operating the "interplanetary power element synchronize system". After setting the system up, the four spheres containing the crystals start glowing before the airship of the Deathgyunos descends. The two robotic figures are shown once more stating that the operation is to start, before the airship reforms itself and opens something similar to a solar sail.
The Black Moon is then shown along with several streams of energy that converge on it. These streams are then gathered by the airship and bundled before they are propagated to the machine below it. Ra Devil then announces happily that he can feel the power of the entire universe flowing through him, before some imp like creatures start the bio-reactor that is powered by the Crystals. It is now that power is drawn from the Crystals which leads Linaly to awaken. Cid's brain starts to glow at it's middle, before an excited Ra Devil how he almost can't stand the wonderful excitement that comes with the wave of energy running through his body.
The scene then cuts to outer space, where we see the pirate's airship. The pirates including Rouge are heavily impressed by the sight of Planet R below them, but appear to be quite puzzled with how they could have lived on a round sphere, with Rouge even stating that they must have been living on the top, as they'd have fallen off if they were down there at the bottom. It is them shown that the airship is being pulled by the Hyriuu along with the Iron Wing, aboard which Valkus shows concern over how Ra Devil is absorbing energy out of the universe. Mid agrees on this topic, while Prettz states that this must be what they needed the Crystals for. Upon looking at the Linaly's earring, Prettz grows even more impatient and eager to save Linaly and asks Valkus if he can not speed the Hyriuu up, something which Valkus naturally can't.
At the same time, Ra Devil's body has started to react to the machine and begun rebuilding himself, a feat upon which the imp like beings on the moon's surface rejoice, stating that their God is finally about to be born. The Hyriuu along with the two airships then finally enter the atmosphere of the Black Moon, albeit at an high speed which causes Pretz to worry; Valkus however says to have faith in the guardian god of Tycoon. However, the Hyriuu is then hit by a lightning bolt soon after that, and starts tumbling to the surface, pulling the airships with himself. Prettz orders Valkus to do something, but the Iron Wings chief can not prevent the fall and as such, the two airships crash on the Black Moons surface.
After the crash landing, the Pirates ship is heavily damaged, leaving Rouge to order her crew to repair it while she goes to the Iron Wing along with two of her Pirates. On the way there, she catches the unconscious and now once more minuscule Hyriuu as he falls from the sky. She tosses him over to her remaining crew, stating that while fixing the ship, they should fix him too.
Ra Devils new and still incomplete body can then be seen rising into the air, while the imp like creatures rejoice as Deathgyunos, god of the universe, has successfully been reborn into their master. Meanwhile, Prettz, Rouge and Valkus are at a loss as to where they can find the enemy, after which Prettz remembers the powers of Linaly's earring. Using it, he tries to mimic her and converse with the spirits by concentrating. He however gets no chance to concentrate sufficiently on it, as soon Mid gets literally shocked due to Cid talking with him in his mind, telling him to head North. The Iron Wing then takes off, flying northwards. This however gets noticed by the robotic figures as their sensors find an unidentified flying object heading towards them.
Due to this, the Iron Wing soon enough get welcomed by the enemy engaging them in battle. The Iron Wings send out their elite troops, however despite their abilities, the Iron Wing gets in the line of fire. This leads to Rouge being hit by an attack, leaving a small scratch on her shoulder from which she bleeds. Enraged by this, Valkus takes up two guns and literally turns into a berserker, shooting at every enemy moving without hesitation. Prettz and Mid can only watch in astonishment as Valkus eliminated the enemies on his own, to which Mid only can say that "Love makes one insane."
Gush then points out the position of Deathgyunos, who is still not fully constructed but nonetheless to open fire at the Iron Wing. Valkus then orders Gush to charge forward with the Iron Wing, something which the second-in-command tries to deny as being far too reckless. However, after Prettz repeats the same order, Gush merely states that he does not take orders from one like him, and pushes the engines to full power. Upon coming nearer, Valkus orders everyone to retreat to the rear before the ship collides with Deathgyunos.
After the ensuing detonations and explosions, Prettz and Valkus decide to split up. While Prettz goes to look for Linaly, Valkus starts searching for the Crystals in the debris. Prettz soon encounters a robot carrying Linaly which promptly open fire on him before attempting to escape. Prettz however quickly catches up and destroys the robot with his Kiku-ichimonji, rescuing Linaly. Linaly however then starts attacking Prettz with a series of kicks, knocking him out before Mid appears. Using a sort of steam coming out from his mouth, Mid lifts the mind control of Linaly, leaving her to notice the unconscious Prettz and wonder who it was that did this to him, effectively having forgotten what she did while being controlled. Another imp like creature more than twice the size of Linaly then appears and tries to apprehend her, but is quickly taken down by Valkus. Prettz then, after regaining consciousness and learning from Mid that Linaly indeed was under mind control, returns her earring to her.
It is then shown that Valkus and his men successfully found the three Crystals, and as such, Rouge suggests that they all should leave the Black Moon now. However, as Gush has to say, the Iron Wing is unusable now. Meanwhile, Mid can hear Cid's voice calling out to him weakly and goes to look for it, finding the enlarged brain of his grandfather in the process. Happy over being reunited with his grandfather, Mid goes to visit his brain and talks with him, promising him to take him home. However, before he can do so, Deathgyunos starts moving once more. Valkus says that he believed the thing to be death to which the monster replies that as it is the truth of the universe, and as such does not know death. Mid then goes off to engage Deathgyunos after asking Prettz to look after Linaly who tells Mid not to go, as he would be killed. Stating that he already is dead, Mid proceeds and actually manages to stall Deathgyunos, buying his friends time to make their escape. However, before they can reach the Pirates airship, an agonized cry of Mid can be heard as Deathgyunos emerges once more.
After clearing the way with another barrage from his guns, Valkus orders Gush to take everyone to safety while he and Prettz will face the approaching Deathgyunos. The two then taunt him while attacking so that they can lure him away from the airship. Linaly and Rouge quickly rejoin them, stating how they could not let the two men alone to face this crisis. Linaly then suddenly starts emitting light from her body just before the Wind Crystal leaves her body, only to make his new home in Prettz just prior to Deathgyunos arriving at their hiding spot. Valkus and Prettz then valiantly attack the self-nominated god, leading to Prettz being easily captured by him. Mocking their inability to harm him and stating that mortals could never hope to defeat a god like him, Deathgyunos then uses electricity to torture his prisoner.
Linaly, worried about her friend, tries to hurry to his side but is too late, as Deathgyunos drops him just before she can arrive. However, Prettz manages to hold on to a steel bar, and while he pulls himself up, Rouge and Valkus open fire on Deathgyunos hand, destroying it. Angered by this, Deathgyunos attacks the fleeing Rouge with an energy beam, leaving her to fall to the ground before Valkus catches her. Prettz and Valkus, both angered by this, then decide to fight instead of running, and charge at Deathgyunos but are quickly taking down by the same energy beams as Rouge.
With the two man covered in debris and unable to fight, Linaly decides to engage Deathgyunos. Demonstrating once more her unusual powers, she forms a platform out of the ground and levitates it to get closer to Deathgyunos face, before preparing an attack. However, before she can perform the attack, Prettz body begins to glow before sending a beam of energy into Linaly, strengthening her powers. Linaly then goes on to summon a whole wave of her chocobos that she throws at Deathgyunos. This fierce onslaught of featherless birds manages to take Deathgyunos down, leaving him to fall to the ground. Already rejoicing over their victory, the party gets surprised by the upper part of Deathgyunos rising yet once more in order to attack them. However, this last stand of Deathgyunos is short lived, as Prettz instantly charges at it and cuts it cleanly into two halves, which both detonate as a result of this final blow.
Following this victory, Mid reappears, apparently being well thanks to being a spirit. He then thanks the party for having helped him free his grandfather, before the old Light Warriors are shown with Cid holding his brain in the middle. Mid then departs alongside his grandfather, but not without telling Prettz that they should meet again once he is dead, to which Prettz replies that they should just take care that Cid's brain doesn't get stolen again. Using Chocobos summoned by Linaly, the party then returns to the Pirates' airship where everyone awaits them already, ready to go back home to Planet R.
Linaly's grandfather can then be heard complimenting his granddaughter as she had proven herself a true descendant of the courageous Bartz. While Linaly and Bartz then explains how she and her friends returned to Planet R, the exact same events are shown with the Hyriuu pulling the Pirates' airship back to the planet, before it shows the party along with Queen Lenna in the Wind Shrine, returning the Wind Crystal to it's rightful place. The tale ends with Prettz then asking the grandfather if he now has a better opinion of him to which he declines, before showing the three of them traveling on the same ship as in the Chapter of the Wind. Linaly's grandfather then asks what happened to the lady pirate, just before Rouge's airship appears to greet them and wish them a safe trip. Prettz then asks how it comes that Rouge went back to being a pirate after receiving so much treasure from Queen Lenna, to which she answers that she has another dependent to be fed on her ship now after all, revealing Valkus who has joined her crew before taking off. The chapter then ends with Linaly, her grandfather and Prettz continuing their journey home and a view ahead to their village, concluding the series.