A few months after the defeat of Death Phantom and the Malefic Black Crystal, Usagi, Ami, Rei, Makoto, Minako and Chibiusa are all enjoying their normal lives. However, new enemies appear out of nowhere and are attacking humans in order to absorb the hoste or souls of their human victims in order to live and sustain themselves on Earth. Can the six Sailor Guardians stop this new, unidentified threat?

Now that a new and mysterious monster has appeared, the Sailor Guardians are bent on finding out by infiltrating Mugen Academy. While battling another of these new monsters called Diamon, Sailor Moon and Sailor Chibi Moon befriend a strange girl with unusual powers. But just what kind of connection does she have with the new enemy?

Usagi and the girls discuss the two mysterious figures they saw, who appeared to look like Sailor Guardians. Luna and Artemis warn the girls to be careful, as they are still unsure whether these two are friend or foe.

The Sailor Guardians defeat Eudial but allow the mysterious Guardian to escape. Still suspicious about Mugen Academy, the girls decide to check out the place again by attending Michiru Kaioh’s violin recital, which is being held on campus.

The Sailor Guardians learn that Haruka and Michiru are Sailor Uranus and Sailor Neptune. However, the two do not appear to be interested in working with the other Sailor Guardians.

The Sailor Guardians must stop a plant called Tellu from stealing the Hostes from humans. Meanwhile, a college student named Setsuna Meioh is investigating the Sankakusu Delta, but she too falls victim to the Tellu plant.

Sailor Uranus, Neptune and Pluto appear before Sailor Moon and the other Guardians to reveal their true agenda. Learning what’s at stake, Sailor Moon and the others offer their help but are rejected by Uranus, causing further tensions.

Hotaru turns into Mistress 9 and takes Chibi-Usa’s Legendary Silver Crystal and her soul as well. To save Chibi-Usa’s life, the Sailor Guardians must head into Mugenzu so that they can retrieve her stolen soul and the Silver Crystal.

The Sailor Guardians fight their way through to find Hotaru, who is in possession of Chibi-Usa’s Silver Crystal. They manage to defeat Kaolinite but must now face Professor Tomoe and his Daimon monsters.

Now that Professor Tomoe and Kaorinite have been destroyed, it is up to the eight Sailor Guardians to confront Mistress 9 directly and eradicate her once and for all. As Pharaoh 90's complete vesselization looms nearer, Hotaru's consciousness is determined to do whatever she possibly can to save Chibiusa and stop Mistress 9 from using her body for evil ends.

Super Sailor Moon and everyone else continue to fight with their memories of Hotaru in their hearts. All attempts to obliterate Pharaoh 90 have failed and the world seems lost, until the awakening and return of a certain person comes to turn things around...for better or worse.

Now that Sailor Saturn has awakened, she has unleashed her strongest and most destructive attack yet and has swung down her Silence Glaive, putting an end to Pharaoh 90 and the whole world itself in the process. But all is not yet lost.