In the future Crystal Tokyo, a small band of discontent citizens have come together to form a rebel team of Senshi called the Oppositio Senshi, who feel that the Sailor Senshi and the Silver Crystal are the source 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 have 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 Senshi, along with Chibiusa go missing.
Sailor Moon meets up with Uranus, Neptune, and Saturn to go look for the missing Senshi. They are told to go Juuban Junior High 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 unleash a devastating attack. Tuxedo Mask is hit by the blast and injured, and Sailor Saturn is injured by a 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 Senshi go 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 are 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 frighten 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 group of Youma who are masquerading as monks. Her counterpart, Nergal, had created a ruby that would paralyze Sailor Mars in order 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 own 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 retrieve 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 Chibusa 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 afterwards, 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 Senshi arrive 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 steals the Rose Crystal and go to the Silver Millennium of the past.
The Sailor Senshi realize 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 in order 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 Senshi later return to the Moon Kingdom in the aftermath of Beryl's attack and are 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 have 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 go to Apsu's palace, where the Oppositio Senshi launch an all-out attack but are defeated. The Sailor Senshi use the Silver Crystal on them and completely rewrite 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 kill Anshar, then revive 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 into 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 Senshi prevail and destroy 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.
Sailor Moon: Another Story, as is the case with most RPGs, has two different well-defined parts: The first is overworld exploration. The game features several locations, the Juuban district being the biggest one, that must be explored in order to progress in the game. However, unlike most other RPGs, most of these locations cannot be accessed after the player has finished all plot-relevant events, making the gameline very linear one. To explore locations, a 2D top-down perspective and grid-based movements for characters are used.
The second is combat and it focuses in tactics rather than action
In the battles in the game, the player uses a team of up to 5 Senshi (or less depending on where in the game the story takes place. In the later parts of the game, the player can choose between any Senshi. However Sailor Moon is almost always required to be in the party, and Chibi Moon is required quite often as well). Each Senshi has 12 EP max (which is received after a few level ups). Several of the Senshi can also use their powers in combination for new attack. For example; Mercury and Chibi-Moon can use a combo attack called Pink Sugar Illusion, which revives all allies.
The main villain of the story was Apsu, a sorceress who sought to alter time so that she could stop Crystal Tokyo from existing, because its existence was slowly killing her. With four disillusioned young girls from Crystal Tokyo (Sin, Nabu, Nergal, and Marduk), as well as Nabu's friend Ishtar, who was accidentally recruited, she created the Oppositio Senshi. Together they formed Hell Destiny, along with Sin's little brother Anshar and his pet Kishar. This band of rebels were convinced that the Silver Crystal needed to be destroyed for the good of the future.
Other villains who appeared during the game were past enemies that Apsu revived by "changing their destinies." These included Queen Beryl, Mistress 9,Black Lady, the Black Moon Clan, the Death Busters, and various Youma, Daimon, and Droids. The Shitennou, now allies to the Senshi, appeared as ghosts and aided them in recovering the Shin no Ishi. Prince Demande and Saphir appeared in the game but were never fought, as both were killed by Sin.
- Sailor Moon
- Sailor Mercury
- Sailor Mars
- Sailor Jupiter
- Sailor Venus
- Sailor Chibi Moon
- Sailor Saturn
- Sailor Uranus
- Sailor Neptune
- Sailor Pluto
- Shaman Apsu - The chief villain in the game, named for the primal being of Babylonian creation myth. Apsu seeks to rewrite history and erase the Sailor Moon legend from time forever, allowing her to stay alive, as she is slowly dying. Transforms into a second form called "Deity of Destruction" (known as Demon Apsu in the fan translation) and attacks with Fin de Siècle, French for "End of the Century."
- Anshar - Sin's younger brother, who she strives to protect no matter what. Named for the sky god, Anshar and Sin play a significant part in the overall plot, particularly when Anshar befriends Chibiusa.
- Kishar - Anshar's pet. What exactly it is however is unknown. It has both a cuter normal form and a larger fierce form that is fought in battle. Named for the sky god's Consort.
- Opposito Senshi - A group of doppelgangers from 30th century Crystal Tokyo, all recruited by Apsu and given powers equal to their counterparts. Each girl has their own motives for joining, but in truth are merely Apsu's pawns. Oppositio is the Latin for opposition.
- Sin - The Oppositio version of Sailor Moon, named for the moon god. Sin blames Neo-Queen Serenity (Sailor Moon) for letting her parents die during the Black Moon invasion, thus driving her entire rage. She attacks with Hells Attack.
- Nabu - The Oppositio version of Sailor Mercury, named for the wisdom god Namu. Attacks with Hell’s Freezing and Berthier's Dark Water.
- Ishtar - The Oppositio version of Sailor Venus. Named after the fertility goddess. Attacks with Hell’s Shower and Calaveras' Dark Beaut Whip.
- Marduk - The Oppositio version of Sailor Jupiter. Named after the king of the gods. She attacks with Hell’s Thunder and Petz's Dark Thunder.
- Nergal - The Oppositio version of Sailor Mars. Named for the fire god. She attacks with Hell’s Flame Bird and Kōan's Dark Fire.
The following monsters of the day are featured in this game as common enemies:
Besides Shaman Apsu and her followers, the following are bosses in this game:
Senshi's EP Moves
Usagi Tsukino/Sailor Moon
- Moon Tiara Action - Damage 1 enemy - 1 EP
- Moon Healing Escalation - Heal an ally - 2 EP
- Moon Spiral Heart Attack - Damage 1 enemy - 3 EP
- Rainbow Moon Heart Ache - Damages all enemies, 6EP. (MoonCup1)
Chibiusa/Sailor Chibi Moon
- Pink Sugar Heart Attack - Damage 1 enemy, 4 EP
- Pink Sugar Heart Ache - Damages all enemy, 6EP. (MoonCup2)
Ami Mizuno/Sailor Mercury
- Sabão Spray - Damage 1 enemy (also lowers their attack. This effect is not mentioned in the flavor text) - 2 EP
- Sabão Spray Freezing - Damage 1 enemy - 3 EP
- Shine Aqua Illusion - Damage 1 enemy - 4 EP
- Mercury Aqua Mirage - Damages all enemies - 4 EP
Rei Hino/Sailor Mars
- Fire Soul - Damage 1 enemy - 2 EP
- Firebird Soul - Damage 1 enemy - 4 EP
- Burning Mandala - Damages all enemies - 6 EP
- Mars Snake Fire - Damage 1 enemy - 6 EP
Makoto Kino/Sailor Jupiter
- Supreme Thunder - Damages all enemies - 1 EP
- Thunder Dragon - one - 3 EP
- Sparkling Wide Pressure - one - 4 EP
- Coconut Cyclone - all - 6 EP
Setsuna Meiou/Sailor Pluto
- Dead Scream - Damages all enemies - 3EP
- Chronos Cyclone - Damages all enemies - 4EP
- Time Stop - Time stops on all enemies for three rounds - 12EP
Michiru Kaiou/Sailor Neptune
- Deep Submerge - Damages all enemies - 3EP
- Submarine Reflection - Damages all enemies - 4EP
Haruka Tenou/Sailor Uranus
- World Shaking - Damages all enemies - 3EP
- Space Sword Blaster - Damage 1 enemy - 4EP
Hotaru Tomoe/Sailor Saturn
- Death Ribbon Revolution - Damages All Enemies - 2 EP
- In the game, Rei still has some romantic feelings for Mamoru.
- This game is closer to following the anime than the manga, containing elements such as the reformed Ayakashi Sisters.
- The anime voice actresses recorded new phrases for attacks that were never seen in the anime, but appeared in the manga, such as Venus Wink Chain Sword and Jupiter Coconut Cyclone.
- For some time, players of this game thought that the game had a glitch: In Sailor Jupiter's chapter, when she arrives to Medias Village, in order to progress in the game she has to visit George's house, talk to his mother and then talk to George. Talking to him first causes the Mishii Village's pendant to not appear, and without it, continuing the quest is impossible.
- The first monster attacks in the jewelry store, just like the first monster in the original anime, second anime, and manga.
- The hidden puzzle pieces in Ami's solo level are able to be collected at a later time. However, the 4 in Mako's solo level must be picked up on the first visit to the level, or else they are unobtainable, making completing the puzzle impossible.
- The game-exclusive character's are named for god's and goddess's from Mesopotamian and Babylonian mythology.