In the Earth Kingdom, Beryl prepared to mobilize the Shitennou and the kingdom's armies to attack the moon. Meanwhile, Serenity and the senshi considered the possibility that Queen Serenity knew about their relationships with the Earth men, especially because of the mentions of Earth she dropped into the conversation that morning. Queen Serenity indeed knew, but was torn about whether to talk about it openly or not. She did not want to take away Serenity's first love from her, but she did worry. Eventually, though, she began to dream about the same thing; of a peace alliance between the moon and earth. In the Earth Kingdom, Endymion tried futilely to stop the fighting and confronted his shitennou when they were on their way to Beryl's room. Despite his attempts to use logic, they remained persistent because of the brainwashing done by Beryl with help from Metalia's powers. He instead chose to go to the Moon himself to warn them, using a magical key that had been passed down through his generation, though he was the first one who managed to use it. Unfortunately, upon arrival at the moon, he was caught by the guards who quickly dumped him in the dungeons. He yelled to everyone who would listen about the incoming attack, though so far no one listened. Except for Luna, who had seen the commotion and recognized him. She quickly informed Serenity and the senshi about his predicament and about the impending attack. The senshi quickly devised a strategy to break into the prison in order to save Endymion and listen to what he had to say. After going through a secret tunnel Mercury had once read about, the senshi found the passage blocked, but Jupiter blasted through it. They arrived in the dungeons and Serenity quickly found Endymion. Mercury froze the lock on the door and Venus broke it, freeing the prince. He was devastated, thinking the explosion meant he was too late, but with some urging and Serenity's presence, he quickly told them about the situation on Earth; that they were attacking the moon soon, and that Beryl had corrupted his generals along with everyone. When they returned to the throne room to find Queen Serenity, she was not there, and neither were the cats. The queen, who had been informed about a prisoner in the dungeon claiming to be from earth, went down to look for him herself using the main passage and missed them entirely. Venus sent the senshi to split up; Mars to command the army, Mercury to help the evacuation process, and Jupiter to take Serenity somewhere safe while she herself looked for the queen. After a brief embrace, Venus left followed by each of the senshi. On Earth, Beryl opened a portal to the moon with Metalia's help and the Earth kingdom people arrived, immediately attacking the citizens of the moon. Serenity asked Jupiter to take her and Endymion to the prayer room in the Moon Palace, and Jupiter barricaded the door behind her once they were safely inside. She ran into Nephrite on her way out and they fought. Similarly, Mercury encountered Zoisite in the city, and Mars, in the midst of battle, was eventually found by Jadeite. Venus finally found Queen Serenity and filled her in on what was happening; the queen was understandably shaken. But she composed herself and immediately started rallying her people and erected a barrier around the palace, where Venus had told her Princess Serenity was being kept safe. As Venus went out into the battle, she found Kunzite. With Metalia's help, Beryl managed to breach the barrier and went straight to the prayer room, spotting Endymion on the roof. Metalia's power destroyed a chunk of the castle and created a hole in the prayer room. Before Beryl could kill Serenity, Endymion jumped back in to protect her. However, Beryl and Metalia were simply too strong; with another wave of power the prince was sent off the edge of the now open room and flung into the sky. Serenity jumped after him, not wanting to lose him. The two struggled to reach each other during the fall but failed. They fell to their deaths inches from each other. The death of their princess hit most of the senshi hard and affected their respective battles. Jupiter was stabbed by Nephrite, but she took him down with her by pulling him close and sending her lightning through them both. He was able to snap out of his brainwashing before they both died. Mercury and Zoisite's fatal attacks hit each other at around the same time and they went down. He, too, remembered who he was before he died. Jadeite, angered by Endymion's death, blamed Mars and killed her. He did not manage to return to himself until after Mars died, but by then it was too late. He was killed by another Earth soldier who saw his change of heart and deemed him a traitor. Venus left her fight to grab the Holy Sword of the Moon and killed Beryl up in the prayer room, but once Beryl was gone, Kunzite followed her up there. They exchanged blows but he eventually overpowered her. Disarmed and pinned, Venus had no other choice but to stab him with his own dagger that he'd once given her. Kunzite sent a blade of energy toward her with his last breath, which killed her, without ever remembering his love for her. Queen Serenity sealed Metalia and wished for the Silver Crystal to reincarnate everyone into a happier future on earth. She knew the seal was not complete and asked Artemis and Luna to find the senshi again and take care of the threat once and for all. She, too, died, having spent all of her energy. Every single one of the moon kingdom denizens' souls were lifted to the air and sent forth to be reincarnated again. Outside the solar system, each of the Outer Senshi's talismans began to glow and transported them to the ruins of the Moon Kingdom. Pluto's Garnet Orb, Uranus' Space Sword, and Neptune's Deep Aqua Mirror joined as one and summoned Sailor Saturn, who then lowered her Glaive and ended the Silver Millennium era in silence.

Sailors Achelois, Nocturnus, Panacea, Varuna and Enyalius followed Sailor Andromeda to her planet (on a mission Sailor Jupiter sent them against Chaos's influence), meeting in mid-air with their new companions : Sailor Sedna and Sailor Callisto. Enyalius greets them first, introducing the others when Sailor Amatheia joins them, seemingly amazed by Enyalius. The last of their group, Sailor Makemake, joins them with a bang, introduction cheery, though slightly exuberant, but Sedna then remarks on the time being precious. Enyalius uses this intervention to bring everyone's mind back on the business at hand: helping Sailor Andromeda in saving her planet. She flies down towards the planet's ground, followed by the others in an arrow formation, readying herself for any probability of battle.

Flying above the city – surprisingly quiet – they finally reach the castle where angry inhabitants seem ready to storm the royal family. Despite the vantage point, some Sailors land while others keep hovering above ground. Amatheia then suggests that she tries reasoning with them, but isn't answered. Andromeda finally notices their presence and flies to them. She feels hope despite her despair at the situation, pressing the matter that this chaotic influence must be destroyed at the source: the eye of the tornado.

Agitation grows. Sailor Varuna begs them to react to the angry mob, but in the tensed atmosphere, Sailor Amatheia's attention is distracted by the rumor of a song carried with the wind. Her strange behavior doesn't go unnoticed, annoying Varuna and unnerving Callisto. Despite their own team growing restless, Enyalius focuses on Andromeda first. According to her, it's not the first time the castle has been sieged, but never had it been this chaotic. She insists again on going to the eye of the storm as soon as possible. Enyalius ponders upon a solution that would get them to the storm without endangering the people locked in the castle when the mobs finally notice them. Mere seconds later, the inhabitants turn their violence towards the group of senshi.

Affected by the chaotic atmosphere, Sailor Makemake utters about the oven, then offers herself to make the first move against the angry mob, irritating Andromeda who makes it very clear that nobody is to hurt any of her people. She prompts the soldiers on the ground to join them out of reach as Sailor Achelois uses her power to calm the spirit of those of her counterparts she can reach. Callisto answers quickly to the mob's threat, taking off to regroup with the others, while Amatheia, plagued with images of her past, starts screaming, startling Makemake who aborts her attempt at traping the mob in her vines. As Enyalius screams to her crew to calm down, the time around them seemingly comes to a stop and everything falls into complete silence.

An old woman addresses them, forcing those hovering in midair to land so she doesn't have to look up. One by one, she gives them objects to help them during their mission, the senshi accepting the gifts. She asks in exchange for this gifts that they get to the tower and get rid of the chaos seed, giving them a last blessing rendering them immune to what were affecting their moods. She also says she boosted their strength and speed for the fights to come and leaves with a last warning : they have 27 hours before the crowd starts to kill each other.

When the old woman is gone, Enyalius orders the others to fly back away from the crowd, asking Andromeda if she is certain the tower is in the middle of the hurricane. As the others obey her command, Andromeda assures her of her conviction, Callisto pushing for their departure.

The group move to the hurricane, the wind getting cooler, harder, more aggressive. They all can fly, but some better than others, so Enyalius worries on how they will all fare and if they all will be able to breach through the hurricane to get to the tower. Varuna is the first to verbalize her doubts about her own capacity to withstand the winds, sharing her fear with Andromeda, not wishing to be left behind. Makemake then intervenes, offering her help and she is soon joined by Achelois who, already knowing that some of them wouldn't be able to fly through, suggests that they fly to the atmosphere, out into space and then back directly into the eye of the storm. Most of them agree and even those who had started to fly through the storm come back to their friends, Enyalius the first to fly in the atmosphere, waiting for the others to join her above the storm.

Sailor Callisto, already in the storm, decides to keep going. Makemake notices the lone senshi, joining her.

Though all the others make it to space – some more comfortable with the cold temperature than others – Amatheia can't help but ask if they're sure that going down is safe, at least from the storm. Enyalius reassures her, pointing at birds flying effortlessly around the tower, but warns everyone to be on their guards. Even if the storm itself isn't an obstacle anymore, the black tower probably has other defense mechanisms. They then all descend back into the atmosphere.

Enyalius storms feet first towards the tower, attempting – quite painfully and in vain – to break through the top of the tower. Her carelessness gives her some minor wounds, but even the small amount of blood it produces seems to attracts the creatures they first mistaken for birds.

Nocturnus calls to Enyalius and Andromeda, seeing what the other senshi wants to warn Enyalius about, and materializes her weapon. As Enyalius flies towards her, she scans the tower for any sign of door or window – but doesn't find any. Amatheia asks the group to cover their ears, trying to use her power to keep the winged eels in place and away from attacking Enyalius.

While most of them are able to cover their ears in time, Andromeda, Varuna and Panacea are not, but only the last two are, like the eels, unable to move, ensnared by Amatheia's song. Enyalius uses the time bought by the siren to try and find a possible entrance. Andromeda, able to resist the song, dives underwater but comes back to Enya without having found anything helpful. Varuna's pleas are enough for Amatheia to help her, the siren slowly guiding the senshi's hands to her ears. Frustrated by the waste of time, Enyalius attacks one of the serpents, killing it swiftly, its body falling in the water.

Meanwhile, Sailor Makemake has stopped trying to follow Callisto, looking for a way to find where exactly she is in the storm. She lets herself fall down towards the water, feeling plants she could communicate with in the water. She hears their voices, one of them suddenly panicking about something coming to eat them, but then laughing it off when it seems to be safe. Callisto, casting a shield around her and noticing Makemake, flies down to meet with her. Makemake, who was approaching the water to talk with the plantlife below, is attacked by two piranhas that fortunately aren't able to bite her. The plant panics again, but calms itself as it notices the danger to be just more piranhas.

Back around the tower, Enyalius kills another eel, much to Amatheia's terror. Trying to help both the senshi and the creatures, she shifts her mind control to get the eels to show them where exactly is the entrance. All of them plunge towards the water, including Panacea who still is under the siren's control. One of the eels bites into Andromeda's shoulder on the way down, and so Amatheia plunges to her aid. Inspired by Enyalius, Sedna tries in turn to kill another of the eels – and misses it, the creature falling too quickly towards the water. Andromeda tries to push the eel off with her power, succeeding, but unable to kill it. It is Nocturnus that reaches the mind controlled Panacea first, yelling while trying to get her hands on the senshi's ears to try and break the spell. She fails, Panacea dangerously nearing the water. Sedna, in turn, tries as well to save the young senshi from a rather unpleasant collision with the water's surface, successfully trapping her in a typhoon of water, creating a pocket of air within it so she could breathe. At the same time, Amatheia follows the eels underwater.

Enyalius, frustrated by Amatheia's doing follows suit, intending to get to the bottom of their problem quickly. The siren loses her wings and legs as she reaches the water, her tail appearing instead as she goes after the eels. A goblin shark attacks and kills two of the three remaining eels, and Amatheia tries to chase it off.

Still in the middle of the storm, Makemake suggests to Callisto that they find a way to the end of this storm, the other senshi agreeing that they need to join forces with the others as soon as possible. Keeping the winds to their left, they are able to make it through the storm. Happy to be reunited with the others, Makemake quickly announces their arrival. Callisto, noticing the rather chaotic surroundings and the missing senshi, asks the others to explain what happened.

Underwater, Amatheia is able to get rid of one shark, but is quickly overwhelmed and knocked out. Enyalius is wounded as well and tries to resurface, but her injuries slow her down. While the senshi above the water wonder what is happening, what to do, or are reunited with the others, Sedna is able to sense the problem going on and uses one of her funnels to try and bring them back. Not only does it succeed at taking Amatheia up, it also comes with a shark, while Enyalius, despite her efforts, finds herself unable to enter the passing funnel, thus left behind. She tries to swim to the surface but is too tired to reach it on time.

Callisto plunges to her rescue, and Makemake uses her vines to try and get them both out of the water while Andromeda keeps searching for something that will tell them how to get past the tower. Callisto and Enyalius are wounded again by the shark, and Makemake's vines close around it instead of them. Callisto casts a stronger shield around them both to prevent any other shark attack and swims harder towards the surface. The piranhas and shark try to attack them again, unsuccessfully, but when they finally breach the surface, Enyalius is unconscious.

Callisto asks for someone knowing CPR, and when Makemake notices that she fished out a shark instead of the senshi, she throws the shark against the tower, cracking it slightly. The creature then falls back in the water, Andromeda flying aside just in time not to receive it on the head. Sedna volunteers herself to try and reanimate the unconscious senshi, in which she is successful. Enyalius brutally wakes up, but expresses her gratefulness towards both Sedna and Callisto. Meanwhile, Andromeda, noticing that Makemake's shark attack weakened the tower, swings her sword at it. She is joined by Nocturnus while Achelois swiftly heals Enyalius, then asks for Amatheia to be brought to her.

It's Sedna who answers Achelois's demand, though reluctantly, bringing the siren senshi to her. Even if she does respect Achelois' decision to revive the fallen senshi, she can't help but share her reluctance, seeing as they were all put through harms because of the siren's song and also doubting she actually was one of theirs. Even though she agrees with her leader on certain points, she makes some remarks, suggesting there be boundaries, but still voting to heal her up. Callisto chimes in, adding that the siren senshi helped them cleanse another planet from Chaos' influence before they arrived on Andromeda.

Achelois quickly revives Amatheia, Sedna using her healing powers to help her in bringing the siren back to health. When she awakes, Amatheia is a first confused then asks for information on their status. At the same moment, the senshi that were attacking the tower are able to dig a hole in it. Though Andromeda does warn the others that there is now a way in, she enters first alone, determined in doing her mission with or without them, soon followed by Nocturnus who asks her to let them help. Meanwhile, Achelois explains to Amatheia that they would like her to communicate with them more instead of deciding on her own on how to act, quickly following the others inside. All the senshi follow inside the tower soon after.

The light is minimal as they discuss whether they will go up or down, Achelois making the answer quite clear as she meditates, finding more enemy down than up, but also finding the seed at the highest point. She counts their enemies and everyone gets immediately cautious when they learn the room they are now in contains 10 of them. Makemake makes the foolish decision of going onward without waiting for anyone, soon followed by Callisto and Amatheia to keep her from harm. As she is going without caution, a monster lurking in the dark has no problem attacking her. Another one goes after Achelois, Enya and Sedna handling this one while Nocturnus attacks the one assaulting Makemake, missing her target. When Makemake tries, however, her vines tear the fish apart.

Callisto uses her Callisto Disk attack in hope of killing one of the sharks attacking them, but instead of slicing her enemy, it hurts Achelois. Enya quickly moves to be at the wounded senshi's side while a Viperfish misses Amatheia and launches itself at Nocturnus and Makemake, who are quickly protected by Callisto who – feeling guilty for hitting another senshi – takes on a more defensive position in front of the two. Enya brings Achelois out of harm's way while Nocturnus searches for the staff that was knocked out of Achelois's hand by an enemy, spotting it and reaching for it. She gets attacked by some strange spikes while down there, feeling strange as the poison invades her body, but not alerting anyone of her situation, not wanting to be a burden. She's still able to get to Achelois and Enya, giving them the staff the healer needs to be able to heal herself. Which she does, to Enya's relief. Meanwhile, Amatheia attacks a monster hidden in the dark, Sedna helps in healing Achelois, and Andromeda attacks the shark again, only to be wounded as well. Sedna uses Ocean Waves to heal her injuries.

Makemake traps two of their foes into her vines, falling asleep as the others plan another attack against the Spire. Enya sends Callisto to the room's ceiling, asking her to knock hard so they would be able to hear from the outside the room they were in. When she finally arrives to the highest point, Callisto feels herself being watched, but cannot pinpoint who or what could be there. Once she hears the knocks, Enya estimates the second floor's location before launching herself at the tower, cracking it once, then twice before Achelois sent an energy spear against the same spot. Nocturnus's injuries from the poison seem to worsen and Panacea finally notices that something is wrong with the young senshi.

Andromeda, instead of helping the others with destroying the spire from outside, tries a more direct approach, going directly to the ceiling to watch Callisto's back, but also to break the ceiling, asking the other senshi to help her in doing so. Unfortunately, their attempt is futile, because stalagmites falling from the ceiling knock unconscious both Amatheia and Nocturnus. Achelois and Enyalius are alerted by all the sound and come to see what happened. It takes them one hour before they can finally get rid of threats and then evacuate the spire. Achelois and Sedna team up once again to heal the wounded soldiers.

Seeing how many of them were hurt over and over again, Andromeda comments on how she cannot ask them to continue helping her in these conditions. Sedna reassures her, refusing to leave, a decision soon followed by all the others. Andromeda finds herself shortly overwhelmed by their support and when she sees it's settled, Enyalius already begins to form a plan for their next attack. She suggests that Amatheia use her song to attract the six enemies present in the second floor and lead them away from the tower so they would be able to make way to the last floor without having to lose more energy fighting. The siren senshi accepts and as soon as Enyalius creates a hole in the tower, she starts to sing, everyone else having their hands against their ears to be protected from the song. The path cleared, they enter the tower, Callisto blocking the entry with a shield.

Once inside, all the senshi team up to make their way through the ceiling, entering a room where they find the siren singing a lullaby to the chaos seed. Amatheia, noticing their victory in her course around the tower to keep the monsters on her trail, knocks on the shield, asking to be let in so she would be able to fight the chaos seed with them. Callisto drops the shield, Amatheia able to enter as well after singing to the monsters to go into the storm.

The fight is started by Andromeda who strikes as soon as the chaos siren is in sight, inspiring the others to do the same. They try to destroy the seed as well, but it soon becomes clear that the siren protects it as a mother would a child, but that they also won't be able to destroy it without killing her. Callisto transforms into a bear to take the fight to their enemy, while Amatheia first tries to protect her. Her try, however, seems to backfire when she ices the chaos seed in order to get it away from the siren. Unfortunately, the ice explodes, hurting her and other senshi around. Her emotions getting the best of her, Andromeda slaps Amatheia, knocking her out. Makemake soon follows on Amatheia's example, protecting the bad siren from the other senshi in turn, but after a chaotic encounter and despite the monsters coming back – soon blocked again by Callisto's shield – Enyalius finally succeeds in killing the siren.

Once the marine creature is gone in goo and dust, they all take turns at hitting the chaos seed, Andromeda being the one finally destroying it. The old woman from the beginning of their journey appears, congratulating them and warning them that the limit of 27 hours included the other seeds as well. It becomes clear now to Enyalius that they won't have any time to rest and that they have to go to Leviathan right away. Many of the current team decides to follow them, but Andromeda stays in order to take care of her newly freed planet, as well as Amatheia and Makemake.

When the group of senshi arrives to Leviathan, they are met there by Ribbon, Leviathan, and Shadow on the planet's watery grounds. Sailor Leviathan, upon seeing them, becomes wary and hostile towards the group, not accepting their help to purge chaos from her planet. Enyalius, Nocturnus, Amatheia and Shadow try to make her see that she should accept them, but when she does, reluctantly so, she also adds that anyone using physical strength to fight should leave the planet while those using magic or being comfortable in the water can stay. In the midst of their meeting, Shadow and Enyalius have some sort of showdown, which finally resolves itself considering the urgency of their mission. The old Crone appears, giving everyone gifts and blessings, then disappears with a strange warning, leaving some of them uncomfortable. Those who are stronger and those who don't know her enough become wary. Not too long after, an earthquake happens, stressing slightly the warriors, pushing them to get on their way as fast as possible. Sailor Leviathan guides them to the mountain, Sailor Oberon linking everyone telepathically, the particular link first annoying both Ribbon and Shadow.

They are attacked on their way to Leviathan's outskirts, Shadow, Achelois and Nocturnus getting rid of it quickly to come to the aid of Enyalius. The situation is slowly getting serious, most of them concentrating on the task ahead instead of their surroundings. Following Sailor Leviathan they soon arrive in the mountain where a large dragon is blocking the way. Instead of killing it, they choose to freeze it, learning that the creature is only there because the agents of chaos would kill its younglings and people if it was to help them instead.

With this new knowledge in mind, they go deeper between the mountains, attacked by eels and squids, the team using their techniques and the new telepathic links to plan their attacks so to make their path easier. A rather smart decision from Enyalius allows Shadow, Sedna, Oberon and her to kill an eel in one timed attack with the help of Callisto attracking their enemy into their ambush. The squid's attack, however, emprisons Shadow between the dead body of an eel and itself, making it harder for them to attack. There are suggestions of using only weapons, but as magic is thrown left and right, some members of their team are hurt. Despite the complexity of fighting in such a small space, they finally get rid of their opponent but have few time to celebrate, an earthquake suddenly shaking their surroundings. Quickly making way to the widest location between the mountains, everyone is able to find a safe spot, except for Amatheia and Shadow, who are buried under solid rock - still alive, but unconscious. At the same time, Enyalius, Achelois, Leviathan, Oberon, Nocturnus, Ribbon and Nix, are faced with two dragons. They fortunately are able to reason with them, and explanations are given on how their enemies work. It's decided that the team should split up, despite some members' reluctance to the plan. Sedna, Callisto and Oberon are sent with the dragons to find the clam while the others stay with Leviathan to fight off the eel and the chaos seed. The team are able to time their attack perfectly through the telepathic link, but the group facing the clam soon encounter their first problems when it seems the clam has mentally connected herself to the other dragons, her pain being theirs – and herself also capable of giving them pain. The situation soon goes to hell and Oberon gets knocked out, Sedna tied up and Callisto unable to actually intervene without hurting someone or putting her own life in the line. Though the difficulties are great with the eel and chaos seed, this team has more luck, able despite the pressure that slowly grows, to attack and finally undermine the eel's operation. With Enyalius wildly striking to kill and Leviathan teaming up with Enoch to destroy the chaos seed, they succeed through lots of fighting and cat-and-mouse chase. Noticing the mental link is down, the group goes to Sedna and Callisto's aid, swiftly overcoming the clam. While Leviathan begs them to let her save the enemy's life, Nix ends up killing her when an explosion hurts some of her companions. Soon after, having too long pushed away the saving of her own planet, Sailor Enyalius succumbs to the chaos corrupting her planet, leaving Leviathan with a promise of doom delivered by the Crone if the senshi wasn't stopped. Some decide to stay and rest with Leviathan and the others prefer to follow Achelois to chase the now rogue senshi.