Usagi and the others try to figure out the identity of Chibi-Usa, the mysterious girl who fell from the sky. Meanwhile, at Rei's school where the school fair is taking place, a new enemy has crept in.

With Sailor Mars in the hands of the Black Moon Clan, the other four Sailor Senshi grow more concerned about where they will strike next. Usagi blames Chibi-Usa and wonders just what she knows about their new enemies. Ami tries to reassure Usagi about the new danger. However, another one of the Spectre Sisters is coming and has set her sights on Sailor Mercury.

Makoto comes to the conclusion that the Black Moon are actually after Chibi-Usa, as opposed to the immeasurably powerful Silver Crystal. The three remaining Sailor Senshi are determined to safeguard Chibi-Usa, as they are sure that she may hold the key to all of their questions and mysteries.

Meanwhile, Petz is causing a deadly disease to spread all over the city that infects Makoto and causes her to become ill.

With Sailor Mercury, Mars, and Jupiter all in the hands of the Black Moon Clan, Minako suggests that she and Usagi talk to Chibi-Usa directly and get the information they need out of her on their new enemies so that they can rescue their fellow Sailor Senshi and eliminate the Black Moon once and for all. But the last of the Spectre sisters' is resolved to avenge her fallen sisters by turning all humans against the people of the White Moon.

In order to help Chibi-Usa save the thirtieth-century future, Sailor Moon, Sailor Venus, Tuxedo Mask, Luna and Artemis all must go to the hidden Door of Space-Time that is guarded by Sailor Pluto; the Sailor Senshi of Space-Time, who does not allow any intruders to proceed further.

Now that they have arrived at the ruined castle of Crystal Tokyo, Sailor Moon, Sailor Venus, Luna, Artemis, and Tuxedo Mask are all surprised to meet a tall young man who bears a strikingly close and unmistakable resemblance to Tuxedo Mask and who reveals himself as the strong-willed King of Crystal Tokyo, and Tuxedo Mask's own future self.

Sailor Moon has been taken captive by the envious Prince Demande, leaving Tuxedo Mask deeply worried about her safety. A distraught Chibi-Usa blames herself for all that has happened since she had secretly taken the mighty Silver Crystal of the future. But will she be able to do something to reverse all of the damage she has unwittingly done?

Chibi-Usa has mysteriously disappeared, which leaves Sailor Pluto, Tuxedo Mask and King Endymion all desperately worried, as she does not have her time key. Meanwhile, Tuxedo Mask is also on a quest to find and save Sailor Moon from the clutches of the Prince Demande, and begs her to lend him and everyone her strength. Meanwhile, Sailor Pluto is gravely concerned about a brewing storm that could rip a hole in the very fabric of space and time itself.

Now under the full control of Wiseman himself, Chibi-Usa has become the Death Phantom's most loyal minion and malevolent Queen of Darkness: Black Lady. Will Sailor Moon and her five dearest companions be able to release Chibi-Usa from the immensely strong negative energy that controls her, or will the past and future both fall to the point of nonexistence at the hands of its own princess and future queen?

With a vindictively evil adult Chibi-Usa now on the side of the Black Moon, the five Sailor Soldiers' are determined to save her. Sailor Moon is ready give up the supremely powerful Silver Crystal of the past, and even her own life, to have the real Chibi-Usa return. But Prince Demande has other plans in store for all that may foil even Wiseman's own plans of world annihilation.

With the supremely powerful Silver Crystals of the past and future in Prince Demande's hands, all is close to the point of annihilation. However, Sailor Pluto may have to pay the ultimate price to create a window of opportunity to allow Sailor Moon and the others to stop Death Phantom, and save both the past and future.