Part One
Months after defeating the Dead Moon Circus, Usagi Tsukino and her friends continue to live peaceful lives as ordinary high school students in the Azabu-Jūban district of Minato, Tokyo. Mamoru Chiba, Usagi's boyfriend, plans to study abroad in the United States. At the airport, Mamoru gives Usagi a ring, but before he can propose, he is suddenly killed by the mysterious Sailor Galaxia, who steals his Golden Crystal and disappears. Unwilling to comprehend Mamoru's death, Usagi believes he boarded his plane and left. After bidding Chibiusa farewell, as she returns to the 30th century, Usagi and her friends attend a concert headlined by popular idol group Three Lights, composed of Kō Seiya, Kō Taiki, and Kō Yaten. During the concert, Sailor Iron Mouse, a Sailor Animamate and member of Shadow Galactica, an empire ruled by Sailor Galaxia and devoted to stealing Sailor Crystals across the galaxy, attacks. The Eternal Sailor Guardians are saved by the Sailor Starlights, a trio of Sailor Guardians from another star system. They realize that the Starlights are the Three Lights, but remain unsure of their motives. Meanwhile, a mysterious child named Chibi-Chibi arrives at Usagi's home, and Usagi and her friends presume she may be related to Chibiusa and accept her presence.
Usagi is disappointed when she fails to hear from Mamoru, and is surprised when the Three Lights enroll at her high school. Meeting Seiya, she learns that the Starlights are searching for their princess, who fled to Earth when Galaxia attacked their planet. They are ambushed by Sailor Aluminum Siren, who kills Sailors Jupiter and Mercury and takes their Sailor Crystals, before being defeated by the Starlights. While Usagi is comforted by Chibi-Chibi, Minako and Rei decide to confront the Starlights to ascertain their motives, and afterward, confront another attacker, Sailor Lead Crow. Lead Crow kills Phobos and Deimos, revealing that the Sailor Animamates are survivors of planets destroyed by Galaxia who have been granted powers of Sailor Guardians. Sailor Moon defeats her, but Sailors Venus and Mars are killed by Galaxia and their crystals are stolen. Their deaths cause Usagi to remember the truth of Mamoru's death.
In the 30th century, Chibiusa notices time distortions affecting the future, but is told to remain by Neo Queen Serenity. In the present, the Starlights notice an incense burner in Chibi-Chibi's possession and discover that it houses their princess, Princess Kakyuu. She emerges, having healed her body, and reveals that Chibi-Chibi is a Sailor Guardian as well. Another of the Sailor Animamates, Sailor Tin Nyanko, attacks Usagi, severely injuring Luna, Artemis, and Diana. They are rescued by the Starlights, who take Usagi to meet Princess Kakyuu. Kakyuu warns Usagi that Sailor Galaxia seeks to control the galaxy by obtaining the Sailor Crystals, especially Usagi's Silver Moon Crystal. On her way home, Usagi encounters Galaxia, who attacks and overwhelms her, but Chibi-Chibi's intervention forces Galaxia to retreat. In her palace, Galaxia reflects on seeking a star worthy of her power and discovering Chaos, an immense embodiment of evil at the center of the galaxy.
Usagi resolves to confront Galaxia in order to regain her friends' Sailor Crystals and restore them to life. Concerned that Sailors Uranus, Neptune, Pluto, and Saturn, who have gone to their respective home bases, may be in danger, she asks for Kakyuu and the Starlights' assistance.
Part Two
Neo Queen Serenity reveals to Chibiusa that the Sailor Guardians are being killed in the past. Chibiusa, joined by the Sailor Quartet, transforms to go help Sailor Moon. Sailor Moon, Kakyuu, the Starlights, and Chibi-Chibi travel to the Outer Guardians' respective home bases, but learn that they have already been killed. They head to Galaxia's base and encounter Sailors Lethe and Mnemosyne. Lethe kills Luna, Artemis, and Diana, blaming the Silver Moon Crystal for causing conflict as she and Mnemosyne reluctantly joined Galaxia after she destroyed their planets. Mnemosyne stops Lethe from killing Sailor Moon, but Sailor Moon asks Lethe to kill her if it will truly bring peace to the galaxy. Lethe, shocked by her earnestness, relents, but Galaxia's henchmen, Sailors Phi and Chi, show up and kill Lethe and Mnemosyne for their disobedience before also killing the Starlights. After convincing Kakyuu they can bring the Starlights back by regaining their Sailor Crystals, they are ambushed by the last of the Animamates, Sailor Heavy Metal Papillon, but are saved by the sudden arrival of Sailor Chibi Moon and the Sailor Quartet. Sailor Moon reunites with Chibi Moon, who assumes that Sailor Moon teleported them to her, but both she and Kakyuu say it was not them, leaving them to speculate if it was Chibi-Chibi.
Sailors Phi and Chi appear again and are defeated, but Kakyuu is fatally wounded and dies during the battle. They are suddenly attacked by the revived Eternal Sailor Guardians and Tuxedo Mask, who are being controlled by Galaxia bracelets. The Sailor Quartet are incapacitated and Chibi-Chibi urges Chibi Moon not to interfere, causing her to question who Chibi-Chibi truly is. Reluctantly, Sailor Moon defeats her friends and arrives at Galaxia's chambers, where they battle. Galaxia flees to the true center of the galaxy: the Galaxy Cauldron, source of all life in the Milky Way. She throws the Sailor Crystals and Tuxedo Mask into the Cauldron, erasing them—and by extension, Chibi Moon—from existence. In doing so, she hopes Sailor Moon's powers will overload from grief and destroy Chaos, which lurks in the Cauldron, thereby leaving her as the sole ruler of the galaxy. Chaos merges with the Cauldron and injures Galaxia, planning to take the Silver Moon Crystal and rule the galaxy.
