In Sailormoon S, the new enemy and the new Sailor Senshi search for the three Talismans, which, when brought together, call forth the Holy Grail which gives the user, the Messiah, the power to save or destroy the world.

The new Sailor Senshi are Tenoh Haruka (Sailoruranus) and Kaioh Michiru (Sailorneptune). Haruka and Michiru are extremely dedicated to their mission, willing to sacrifice anyone, including each other, in order to find the Talismans and prevent the destruction of the world from occuring.

The villains are called the Death Busters. Led by Tomoe Souichi and Kaolinite, they are basically mad scientists (in a sense) bent on finding the Talismans, which are sealed in certain pure heart crystals that some people possess. They use daimon eggs to create daimons to attack people and take the heart crystals.

The story begins with Rei receiving visions of the Silence, which is the event that will happen if the Talismans fall into the hands of the Death Busters, which Haruka and Michiru want to prevent. In the first two episodes of S (90 and 91), the Sailor Senshi come into first contact with the Death Busters and the heart crystals. Usagi's powers also become ineffective, and in 91, with the power of love between her and Mamoru, she gains a new powered up brooch and rod. The Inner Senshi also for the first time meet two new Sailor Senshi, Uranus and Neptune, who remain shadowed until episode 92. As Outer Senshi, Uranus and Neptune do not wish to have the Inner Senshi interfering with what they consider their business. They also correctly believe that the Inner Senshi do not have what it takes to save the world; when a person's heart crystal is removed, the person dies, so the three Talisman carriers will die when the Talismans are extracted.

Most of the episodes following involve the development of the relationships between Haruka and Michiru and the other girls as well as Uranus and Neptune with the Inner Senshi. Each heart crystal extracted fails to deliver any of the Talismans; even Usagi's, which shines extremely brightly because of her purity, does not have it. Usagi and the Inners receive a shock when Chibi-usa reappears in S to save Moon and Mars as SailorChibimoon, the pretty sailor suited soldier-in-training. Though her antics annoy Sailormoon, Chibi-usa does play a much larger, important role later in the season.

In episode 109, the Outers and Inners discover each others' identities which creates a major strain on their relationship. Eudial, one of the Death Busters, also learns of their identities, and using this information, she finds out that Haruka and Michiru are carriers of the Talismans, as shown in episode 110. They almost die, but in episode 111, Meioh Setsuna, Sailorpluto, arrives announcing that she has the third Talisman and saves the other Outer Senshi. The Holy Grail is formed, and upon touching it, Sailormoon temporarily transforms into SuperSailormoon.

Tomoe Hotaru, the daughter of Tomoe Souichi, becomes friends with Chibi-usa in episode 112. She has been cultivated by Tomoe to have an entity, Mistress 9, live inside of her. The other Outer Senshi soon discover that Hotaru is actually Sailorsaturn, the senshi of destruction who is destined to destroy the world, and they attempt to kill her. However, the Inner Senshi intervene, and Hotaru is whisked away before anything can happen. Hotaru does not become Saturn as the Outers fear though; after swallowing the kidnapped Chibi-usa's heart crystal, she transforms into Mistress 9, a Death Buster. This leads to the final confrontation between the Sailor Senshi and the Death Busters.

The three Outer Senshi attempt to infiltrate the school, Uranus and Neptune being the only ones who manage to get inside due to Pluto's sacrifice. Inside, they use their Talismans to destroy the daimon that had possessed Tomoe. They then try to kill Mistress 9 as well but Sailormoon takes the attacks, claiming that Hotaru is still alive. Mistress 9 tricks Sailormoon into giving her the Holy Grail and uses its power to draw Master Pharoah 90 to Earth. This destroys the Holy Grail. Mistress 9 is triumphant until Master Pharoah 90 blasts her. Because of this, Hotaru eventually overcomes the weakened Mistress 9 with her own inner strength, becoming SailorSaturn. Saturn returns Chibi-usa's heart crystal to the girl before going off to battle with Master Pharoah 90. Sailormoon, distraught, uses the power of the other Sailor Senshi to transform into SuperSailormoon and goes after Sailorsaturn. In the end, they destroy Master Pharoah 90 and return peace to the world. Hotaru is reborn as a baby and returned to her father. Haruka and Michiru, after battling Usagi and acknowledging her as their princess, leave.

And the episode after this, Neo-Queen Serenity sends another letter into the future asking for Chibi-usa to return home. Chibi-usa was actually sad to go. But the girls thought that she would want to go, so they pretended that they were happy for her, which depressed Chibi-usa even more. Chibi-usa disappeared into the future, only to return a couple minutes later with another letter saying that it was okay if she stayed longer. Usagi was very relieved.