In the future Crystal Tokyo, a small band of discontent citizens has come together to form a rebel team of Senshi called the Oppositio Senshi, who feel that the Sailor Guardians and the Silver Crystal are the sources of all of Earth's past battles. Together with a mysterious woman named Apsu, they desire to twist time and change the destiny of the Earth.
In the present day, the Sailor Senshi are enjoying peace now that the Death Busters had been defeated. However, strange things begin happening in the city. Previously defeated Daimons, Droids and Youma appear throughout the city. A visit by Ryo Urawa reveals a cryptic statement that the past and future are being replaced. The strangeness doesn't end there - Hotaru grows from a baby into a child in a matter of minutes, Rei sees strange apparitions in the fire, and then the four Inner Sailor Senshi, along with Chibiusa goes missing.
Sailor Moon meets up with Uranus, Neptune, and Saturn to go look for the missing Sailor Senshi. They are told to go to Juban Public Middle School and rescue Sailor Mercury, Sailor Mars, Sailor Jupiter, and Sailor Venus, who were trapped in illusions. On the roof, they find Chibiusa being held captive by Sin, the leader of the Oppositio Senshi. Sin demands that Sailor Moon gives her the Silver Crystal and Sailor Moon accepts, but Tuxedo Mask refuses and in return, the Oppositio Senshi unleashes a devastating attack. Tuxedo Mask is hit by the blast and injured, and Sailor Saturn is injured by an energy beam from Sin before her group leaves.
After taking Mamoru to his apartment to recover, the Senshi are greeted by the spirits of the Shitennou, no longer under Beryl's control. Each gives one of the Inner Senshi their "Yin" stone, which will lead them to the matching "Yang" stone. When all four of these stones are brought together, the location of Mamoru's crystal, the Rose Crystal, will be made apparent, and when all five stones are in the same place, Mamoru will be healed.
Each of the Inner Sailor Senshi goes on a solo mission to locate the Yang stones: Sailor Mercury to Switzerland, Sailor Jupiter to Canada, Sailor Mars to Tibet, and Sailor Venus to Turkey. Each is followed by her counterpart of the Oppositio Senshi, who is also looking for the stones. Usagi stays in Japan to take care of Mamoru, and Chibiusa secretly heads out to look for the Rose Crystal, which the Shitennou believe is somewhere in Japan.
After Sailor Mercury arrives in Switzerland, a large crowd of Youma frightens her and she backs away and accidentally falls off a cliff. She lands in Kainess Town, located under a gigantic glacier. Hans, a local villager, finds Mercury passed out on the ground and takes her in. Together, Hans and Mercury nurse Hans' mother back to health, find Zoisite's Yang Stone and defeat Mercury's counterpart, Nabu. Nabu reveals that she joined the Oppositio Senshi because the Sailor Senshi of the future failed to protect the Earth with the Silver Crystal.
Sailor Mars arrives in the town of Lasa in Tibet where she explores a temple; however, she is attacked by a group of Youma who are masquerading as monks. Her counterpart, Nergal, had created a ruby that would paralyze Sailor Mars to stop her from interfering. A man named Faregg saves her and takes her to the village of Yaga but later becomes captured. Subsequently, Sailor Mars embarks on her journey to retrieve Jadeite's Yang Stone and to rescue Faregg which culminates in an encounter with Nergal, at which time Nergal reveals that she joined the Oppositio Senshi because she desired to become as strong as a Sailor Senshi with her power.
Soon after Sailor Jupiter arrives in Canada, a man named George is enticed by the smell of her dinner, and as a token of appreciation for Sailor Jupiter's food, he takes her into the hidden village of Medias. Here, and in the neighboring village of Mishii, Sailor Jupiter helps George and his lover, Mary to be engaged and mends the broken friendship between the two villages. Along the way, she meets her counterpart, Marduk, and retrieves Nephrite's Yang Stone. Marduk reveals that she joined the Oppositio Senshi because billions of people died for the sake of the Silver Crystal, and purified people have no free will or negative emotions. Unlike the others, she recruited herself.
Sailor Venus finds herself in an underground village in Turkey, Rias, where the entire population is male and completely obsessed about Sailor Venus' arrival, showering her with marriage proposals and gifts. After her counterpart, Ishtar, accidentally knocks over a sacred statue of Kunzite and thus turns the villagers into stone, Sailor Venus travels to the nearby village of Sariel, populated with only women. Venus eventually learns about her history in this village and finds Kunzite's Yang stone and Ishtar in a giant airship called the Ark, owned by her past self. After Venus and Ishtar fight, Ishtar reveals that she was accidentally recruited at the same time as Nabu.
Back in Tokyo, Chibiusa heads to Mugen Academy with Momoko in hopes of finding the Rose Crystal. Sin, who placed a small mind spell on Chibiusa, lured her to Mugen Academy even though the Rose Crystal was not there. Anshar, Sin's little brother, let his memory be erased so he would not know of the plan to let Chibiusa lead them to the Rose Crystal. Chibiusa and Momoko are attacked, and though Anshar saves them, Momoko is poisoned. After Anshar cures Momoko, Sin pretends to attack Chibiusa, but the brainwashed Anshar believes that he is supposed to protect Chibiusa, and he takes her to where she believes the Rose Crystal is. Once they land, Anshar falls unconscious, leaving Chibiusa stranded in a forest.
After being informed of the situation by Momoko, Usagi decides to go to Mugen Academy to look for Chibiusa, however, she instead faces Professor Tomoein his lab, who reveals that Hotaru's destiny has also been changed and has now reverted to the identity of Mistress 9. Sailor Moon defeats Mistress 9 and revives Hotaru as Sailor Saturn, and the two of them defeat Prof. Tomoe, though they are unable to change his destiny when he dies once again. After locating Sailor Uranus and Sailor Neptune, they all teleport to Chibiusa's location.
As the Sailor Senshi and Anshar explore the forest, they find a cave and are attacked by the DD Girls, who are again protecting their revived master Queen Beryl. After an initial battle, Beryl uses the ambient energies in the cave to transform into her Super Beryl form and become invincible, but Sailor Moon and Sailor Chibi Moon combine their Silver Crystals to weaken Super Beryl and destroy her. Shortly afterward, the Senshi find the Rose Crystal, but Anshar betrays them and takes the crystal to his sister Sin.
Later, all the Senshi meet in Mamoru's apartment to plan their next move. To their surprise, Mamoru is healthy again but can no longer transform. It is then decided to find Sailor Pluto. When the Sailor Senshi arrives at the Space-Time Door, they find Sailor Pluto, who tells them not to enter the door. However, she is revealed to be Nergal in disguise when she mistakenly calls Chibi Moon "Princess" (which the real Sailor Pluto never does). The real Sailor Pluto is found trapped deep within the dimensional maze beyond the door and is rescued.
Meanwhile, in the Crystal Tokyo era, Apsu tells the Oppositio Senshi that she no longer needs the power of the Silver Crystal to alter reality, because stealing the Rose Crystal was enough to keep Crystal Tokyo from existing. However, Apsu accidentally resurrects the Black Moon Clan using her fate powers, and they steal the Rose Crystal and go to the Silver Millennium of the past.
The Sailor Senshi realizes that they no longer have any memories of Princess Serenity at all, suggesting that someone has altered the time stream. After some debate, all of the Senshi decide to go back in time to the Silver Millennium to find Sin and the Rose Crystal. Their trip is briefly delayed by the arrival of the Black Moon UFO and the Spectre Sisters, who the Senshi reluctantly defeat. Upon arrival in the Silver Millennium, the Senshi locate the Ark and activate it, allowing them to travel the world quickly in their search for Sin.
While visiting the Earth Kingdom in the north, Sailor Moon disguises herself as a servant girl and explores the palace. She meets Beryl, who is currently a Sage for the Earth Kingdom and has not yet joined Metalia, and also witnesses her past self and Prince Endymion having a conversation. Finally, up in the Moon Kingdom, Sailor Moon meets Queen Serenity herself, who recognizes her daughter through her disguise. Queen Serenity says that she is fully ready to accept her fate now that she sees her daughter and her granddaughter. Sailor Moon is upset by the knowledge that her mother and everyone in the Moon Kingdom will soon perish but knows that there is nothing she can do to change her destiny.
The Sailor Senshi later returns to the Moon Kingdom in the aftermath of Beryl's attack and is greeted by Prince Demande, who threatens to alter the future by tampering with Princess Serenity's corpse. Sailor Moon allows herself to be taken prisoner by Demande in exchange for her past self's safety. The other Senshi are then met by Saphir, who begs them to stop his brother from making a deadly mistake. Deep in the basement of the palace, Sin kills Demande as payback for murdering her parents in the Black Moon invasion, then attacks the Senshi before running away. With Sailor Moon rescued and the Rose Crystal recovered, the Senshi return to the present. However, before they leave, the Oppositio Senshi replace one of the Rainbow Crystals that make up the Silver Crystal with a fake, ensuring that it will weaken over time.
Back in Tokyo, the Oppositio Senshi has abducted Usagi's little brother Shingo to lure the Senshi into a trap. The Senshi and Tuxedo Mask follow them to the Space-Time Door, where Fiore stands to block access. Tuxedo Mask stays behind to fight off Fiore while the Senshi go through the door into Crystal Tokyo. Upon arrival, they find a powerful force field blocking access to the palace because the Silver Crystal is now weakened, and so they split into two teams: one to rescue Shingo and one to get into the palace.
The first team goes to Apsu's palace, where the Oppositio Senshi launch an all-out attack but is defeated. The Sailor Senshi uses the Silver Crystal on them and completely rewrites their original personalities, making them perfectly happy. However, Sin refuses to leave Apsu for the sake of protecting Anshar and escapes. The remaining Senshi disable the force field by defeating the Witches 5, then enter the palace to find and fight Anshar. Anshar refuses to fight, but Apsu forces him to go berserk; the Sailor Senshi kills Anshar, then revives him with the Silver Crystal.
Finally, the Senshi return to the Space-Time Door to find a trail of rose petals leading inside. With Tuxedo Mask her prisoner, Apsu meets the Senshi and tries to convince them to give in to her power by promising them their dream lives. Sailor Moon refuses, and she and the other Senshi fight back.
Apsu is seemingly defeated, but Sin locates the dying sorceress begging to live. She forces Apsu to absorb her power, whereupon Apsu transforms into the monstrous Deity of Destruction and tries to destroy everything. Faced with the overwhelming odds, the Sailor Senshi prevails and destroys Apsu. Sin is allowed to live and is reunited with Anshar and the Oppositio Senshi, who comfort each other saying they did their best; because of Apsu, they are now all a strong team and strong friends, and they leave without looking back at the Sailor Senshi. (If Sailor Chibi Moon's team had to take over for Sailor Moon, an alternate reality is created in which Sin is forced out of the Deity, and the timeline is altered so the battles never took place, nor does Anshar recognize Chibiusa.) The girls bid farewell to Setsuna at the Space-Time Door. Back at the Tsukino residence, Hotaru reverts to a baby once more, and Haruka and Michiru leave the other Senshi, hoping they will not have to meet again to fight. Minako, Makoto, Rei, and Ami all head for home, after the latter, reminds Usagi to study. With the destiny of the world resetting itself to normal, the Senshi are ready to face a new day
