Life gets a little complicated as the Death Busters go around stealing heart crystals out of victims with pure hearts. Not only that, but there are two new Sailor Senshi! However, they don't seem to be on the same side... The new senshi go after the heart crystals, but if it isn't a holder of a "talisman," they give it back to its owner.

Soon Usagi and Tuxedo Mask are involved in an attack. Usagi holds Tuxedo Mask's hand, and out of their love forms the Spiral Heart Moon Rod. Her brooch transforms, and she is able to transform into Sailormoon again!

As the story advances, the girls befriend two girls named Michiru Kaioh and Haruka Tenoh. Haruka is very boyish and likes to race cars. Michiru is very elegant, intelligent and talented in both music and art. Kaolinite goes after pure heart crystals with the daimons, but a holder of a talisman still eludes her. All the girls end up being attacked for their pure hearts. Sailor Neptune and Uranus continue to go after each heart crystal for the talisman.

Kaolinite is finally put out of the picture, and Professor Tomoe calls upon the Witches 5 to take up where she failed. Still using daimons, Eudial is the first witch to try her hand. At one point, the daimon of the day has Sailormoon and Mars caught in drums. Just as she was about to beat them, a Pretty Soldier in Training appears!! Dressed adorably in pink (what else?), the little munchkin has returned as a Sailor Chibimoon!! Using an ill-effective "Pink Sugar Heart Attack!" she manages to divert attention so that the others may get free.

Now joining the adventures, Sailor Chibimoon and the other's continue to battle the Witches 5. Chibi Usa makes friends with a girl named Hotaru, who has the special ability to heal. We later find out that she is Professor Tomoe's daughter. Eudial soon discovers who is the holder of a talisman, and the Uranus and Neptune are surprised to find out it's themselves!! Just when you think it's over, Pluto returns! She takes the garnet orb out of her staff, and it is one of the talisman also! She takes the other 2 talisman, and returns the heart crystals to the senshi. Just when you think nothing else could possibly happen, Sailormoon receives a secondary transformation by using the holy grail! She can now become Super Sailormoon!!

Now the goal of the Death Busters is to find pure heart crystals to feed to the messiah to awaken her. Soon we learn that Uranus, Neptune and Pluto are the outer senshi, who guard the solar system from danger. When they awakened as senshi in this time, the enemy had already came. The Witches 5 successfully eliminate each other one after another, each wanting a turn at finding pure heart crystals.

Soon it's Cyphrine who is left, and she calls upon all the students of the Infinity Academy to come so she can steal their heart crystals. The senshi go to the Academy. Meanwhile, Chibi Usa went to visit Hotaru's house, when Kaolinite (back from the dead) steals her away so she can get the brightest and purest heart crystal. The senshi begin to fight Cyphrine, only to find a surprise named Ptilol! So it turns out that the last of the Witches 5 is actually two twin witches. Together, they are unbeatable. However, the senshi trick them into blasting each other, and they are finished! The senshi arrive to the professor in time to see an unconscious Hotaru swallow Chibi Usa's heart crystal!!

The messiah awakens as Hotaru's body transforms into Mistress 9. The Academy begins to fall apart, so the senshi take Chibi Usa's body and leave. Mamoru keeps Chibi Usa alive by holding her and sharing his energy. The outer senshi leave, saying they must destroy Mistress Nine. The inner senshi decide they must fight too, but for what they believe in, which is winning the war without anyone being sacrificed (meaning Hotaru).

They are greeted by hundreds of daimons oozing out of the building. Meanwhile, the outers are in a helicopter over the building. They are considering going through the opening on top, when they are blasted. Pluto uses her "taboo" power of stopping time to save Neptune and Uranus. She disappears. Neptune and Uranus enter the building. Mistress 9 feels their presence and sends "daimon Germatos" (Professor Tomoe) after them, while she gets the holy grail. He reaches the two outer senshi and the daimon leaves the professor's body. It is attacked by Uranus and splits into a million new daimons. Meanwhile the inner senshi are fighting off the daimons, when Mistress Nine reaches through a portal and grabs Sailormoon. Without Sailormoon, they can't teleport in to help, so they use all their strength to keep the daimons from advancing further. The outer senshi are losing their battle until Pluto's voice is heard, and their talismen appear! Now the duo finishes it off and goes to the Messiah of Silence.

Mistress Nine had trouble controlling the spirit of Hotaru within. Neptune and Uranus blast Mistress Nine, but Sailormoon jumps in the way. Mistress Nine ties the two senshi up to a statue. Then she asks for the holy grail. Suddenly Hotaru calls through "Papa!" Then she says that she needs the holy grail. Sailormoon gives it to her, much to the distress of the two outers. Mistress Nine regains her strength, and puts the holy grail into a chamber to call upon Pharaoh 90, who will bring the silence. Mistress Nine gloats that Sailormoon can do nothing since she is now unable to make a secondary transformation.

Hotaru calls out to her father again, asking him to help her get out. Professor Tomoe holds her and cries saying that he doesn't know how to help. His tears revitalize Hotaru's soul. The sign of Saturn appears on her forehead, and Mistress Nine's body dissolves. The image of Sailorsaturn appears before Mamoru and Chibi Usa, and she returns Chibi Usa's heart crystal. She then returns to Sailormoon, who is being yelled at by the outer senshi for letting the silence come. Saturn thanks Sailormoon for protecting her body, and then says that she must go to stop the silence. Sailormoon wants to help, but Saturn says that since she cannot transform into Super Sailormoon, she won't even be able to go through the barrier. Sailormoon asks what will happen to Saturn in there, and Saturn says that as the Soldier of Destruction, she has the power to destroy, but that even she cannot escape it. Saturn does a back flip into the dome where Pharaoh 90 is.

Sailormoon is upset and keeps trying to do a secondary transformation, but it's all in vain. The inner senshi feel Sailormoon's struggle and begin concentrating on her. Their tiaras begin to glow, and soon the outer's tiaras are glowing as well. All of the colors appear in Sailormoon's tiara, and then she transforms into Super Sailormoon. With her transformation, Sailormoon goes through the barrier. There is soon a large explosion. The entire building collapses, and everyone is seen outside the building. From a sparkle of butterflies in the sky comes Sailormoon, holding a baby Hotaru. The outer senshi take the baby and leave. The inners help Sailormoon.

Next we see everyone with Chibi Usa. She is upset because she wants to know if Hotaru is ok. No one knows where she is. Later she sees Professor Tomoe with a baby. He says the name is Hotaru, and Hotaru happily reaches for Chibi Usa. Chibi Usa is very happy to know that Hotaru is alive and well. End of Season 3!