Rei has a vision of the Silence, which is basically total destruction of all life on Earth. A strange daimon shows up and steals people's heart crystals (which are found in people with pure hearts), but when the Senshi are fighting it, two mysterious figures show up and examine it saying "it isn't a Talisman". The Senshi have no idea who they are until later.
The Deathbusters appear, at first consisting of Professor Tomoe and Kaolinite, and later the Witches 5. They looking for the "Talismans" which are supposed to form the Holy Grail. They are sealed inside the three purest hearts. They need it in order for their Messiah of Dark, Mistress Nine, to summon a being called Master Pharoah 90 to Earth to bring about the Silence.
Not long after, the Senshi meet a cute "boy" named Haruka and Minako and Usagi immediately fall in love with "him". They also meet a pretty girl named Michiru, who they realize is Haruka's girlfriend. They follow Haruka around all day. Eventually, Haruka tells them that "he" knew they were there the whole time. They ask Haruka if Michiru is "his" girlfriend, and Haruka looks stunned and hints that she is. Minako and Usagi look heartbroken. Michiru comes up and they ask her if she's Haruka's girlfriend, and she replies (in English!) "No," but refuses to look them in the eye (sense a lie there??) Eventually, another daimon shows up, so the group splits up. Moon and Venus transform to attack it. Haruka and Michiru, on a motorcycle, chase down the daimon and stop it, then disappear somewhere. Moon and Venus appear. The two mysterious figures show up again and reveal themselves to be Sailoruranus and Sailorneptune. Later that day they are at that one restaurant they go to a lot, and Michiru shows up with a tall girl with short blond hair. The senshi ask where Haruka is (Makoto asks "where's the boy who's supposed to look like my senpai?") and Michiru gestures to the girl next to her, who tries unsuccessfully to look innocent. The Senshi freak out, and Usagi says "I always thought Mamo-chan was better anyway".
Uranus and Neptune never work with the other Senshi. Uranus and Neptune are also looking for the Talismans, and they are looking for the Messiah of Light. The Inner Senshi all have their heart crystals extracted by the Deathbusters (but they are returned). Uranus and Neptune always show up to see if the heart crystals are the Talismans.
Chibi-Usa reappears as Sailorchibimoon. She says her mother sent her back in time to learn how to be a Senshi. The Inner Senshi learn that Haruka and Michiru are Uranus and Neptune. They in turn learn that the five girls that they've been hanging around with are the Inner Senshi. Eudial, the current antagonist, learns all the Senshi's identities, but keeps them a secret. While at their apartment, Eudial calls Haruka and Michiru and faxes a map, telling her to meet her at the Marine Cathedral since she's discovered who has the Talismans. Haruka and Michiru take Usagi's brooch so she can't come after them as Sailormoon, telling her she'll die if she tries. At the Cathedral, Neptune is captured. Uranus runs to rescue her, but these energy arrow things shoot her and stop her from running across the floor. Eudial takes her gun and tells Uranus that she has a Talisman as well as Neptune and that she'll take Uranus's first. Neptune breaks free and runs to protect her, even though she's shot by the arrows. Eudial extracts Neptune's Talisman, but then Usagi appears and knocks her over the edge of the floor into the basement. Uranus shoots herself with the gun to release her Talisman, despite Usagi's pleas. The other Senshi show up and then Sailorpluto reappears. Pluto has one of the Talismans too, and she revives Uranus and Neptune by seperating their heart crystals from their Talismans. They use their Talismans to summon the Holy Grail. Sailormoon takes it and becomes Supersailormoon. Eudial tries to take the Holy Grail and fails. She goes off a cliff when Mimete, another of the Witches' 5, sabotages the brakes of her car.
Chibi-Usa meets a girl named Hotaru Tomoe (later revealed to be Professor Tomoe's daughter) at the park, and later she and Usagi go to Hotaru's house.
After awhile, the Outer Senshi (Uranus, Neptune, Pluto) realize that Hotaru is Sailorsaturn, the Dark Messiah, and try to kill her. It doesn't work though. Professor Tomoe captures Chibi-Usa and Hotaru swallows her heart crystal, and her body is taken over by Mistress Nine, who had possessed her. Mamoru keeps Chibi-Usa alive by giving her some of his life energy.
Mistress Nine procedes to summon up a lot of daimons which the Inner Senshi battle, and then later capture Uranus and Neptune, using them to taunt Sailormoon. Professor Tomoe is there as this is all happening. The daimon that possesses him leaves him. Mistress Nine tricks Sailormoon into giving her the Holy Grail, and she summons Master Pharoah 90. Uranus and Neptune are not too pleased with Sailormoon ^^; . Hotaru eventually starts regaining control of her body and disintegrates herself! She reappears as a ghost in Sailorsaturn form and gives Chibi-Usa her heart crystal back. She then goes to Sailormoon, who is in some wreckage with Neptune, Uranus, and Professor Tomoe. She tells them she's going to go defeat MP 90. They aren't able to do anything to stop her and she goes off. Sailormoon tries repeatedly to become Supersailormoon. She finally succeeds, and also goes off into MP 90. There are signs of a battle and then she comes back out carrying Baby Hotaru in her arms.
Haruka and Michiru take care of baby Hotaru, and Chibi-Usa worries about her. They return her to the injured Tomoe. Uranus and Neptune face off against Sailormoon, and they almost win, but Sailormoon started shining bright and they are forced back. They finally accept her as their future queen, then leave.
Chibi-Usa was going to go home, but she then decided to stay since everyone wanted her to.