Shortly after Sailor Moon defeated Galaxia, Darien and Serena were married and she bore a child, Serena (or Rini) for short.
Then, six years after the final battle with Galaxia, when Serena was twenty-two-years old, a ecological disaster froze the entire Earth. The people of Earth fell into a state of dormancy and they slept for nine-hundred years.
When the 30th Century came, the power of the Silver Imperium Crystal awoke Serena. She used the crystal's powers to unfreeze the Earth and its people. Serena created a peaceful city to match that of the Moon Kingdom from long ago. This city was called "Crystal Tokyo" and Serena became its ruler as Neo-Queen Serenity. Darien became its king as King Endymion and Rini became its princess as Small Lady. The Sailor Senshi became the guardians of the new city. Neo-Queen Serenity attempted to purify every person on Earth with the Silver Imperium Crystal. Those who refused to be purified were banished to a rogue moon called "Nemesis".
70-85 years later, Small Lady entered the chamber where the Queen kept the Silver Imperium Crystal. She admired it and thought that if she borrowed it, she would become "a real lady like Mommy". When she touched it, it began to glow and all of a sudden disappeared.
At that same moment, the evil and exiled people of the Nemesis, known as the Dark Moon Family, attacked Crystal Tokyo. Without the Silver Imperium Crystal's power, Crystal Tokyo's defenses failed. The Sailor Senshi attempted to fight them off but they were very strong. Neo-Queen Serenity, realizing the crystal was gone, panicked and went outside where the fighting was taking place to look for Small Lady. As soon as she stepped out of the palace, the Dark Moon people attacked her. The Sailor Senshi, in order to protect her, encased her in a cocoon of quartz and she fell into another state of dormancy.
She was taken into the palace and the Senshi found Small Lady in the palace. The King and the Senshi continued to fight but they were in need of the Silver Imperium Crystal and its power. The crystal was no where to be found and Small Lady was afraid to tell them what had happened.
The Sailor Senshi were defeated by the Dark Moon and the King was badly injured. With the help of Sailor Pluto, as Luna-P, Small Lady traveled to the past (present day Tokyo) to seek help from the Sailor Moon of the bedtime stories her father told her. When Small Lady realized that Sailor Moon had a Silver Crystal also, she hoped that, since the Silver Imperium Crystal of the 30th Century was lost, perhaps Sailor Moon's crystal would work.
Though the Dark Moon family followed her to Tokyo and tried to capture her, Small Lady returned to Crystal Tokyo with the Sailor Senshi, Tuxedo Mask, and Sailor Moon of Tokyo. They won a significant battle against the Dark Moon but, during it, Small Lady was tricked into joining the Dark Moon people. Her growth was accelerated into a young adult, calling herself "Wicked Lady" and her powers, which were naturally strong, became dark from the Dark Moon Crystal. The Senshi returned to the past, where the final battle against the Dark Moon was to be fought.
The Sailor Senshi, knowing that Wicked Lady was their beloved Rini, did not fight her as hard as they could and Wicked Lady easily defeated them. She tried to kill Tuxedo Mask first but Sailor Moon tried used the power of the Silver Imperium Crystal to stop her. The Dark Moon's power of Wicked Lady was too strong and the crystal had only a little effect, but the use of the Silver Crystal was enough to give Neo-Queen Serenity the power to channel herself through Sailor Moon.
Sailor Moon became Neo-Queen Serenity and reminded Wicked Lady of the good childhood she had. Wicked Lady realized the lies that the Dark Moon had fed her, breaking the spell they had cast, and she turned back into Rini. Neo-Queen Serenity also turned back into Sailor Moon.
Sailor Moon became Neo-Queen Serenity again and fought the Wiseman of the Dark Moon but his powers were too strong. It began to appear that she was going to lose. Small Lady was very sad, saying that it was all her fault that this was happening. She began to cry and the first tear that she cried turned into the Silver Imperium Crystal. She realized then that when she had touched it, the crystal had gone into her body. She turned into Small Lady and, with Tuxedo Mask's permission, she joined her mother. Using both the Silver Imperium Crystal of Tokyo and of Crystal Tokyo, they defeated Wiseman and the Dark Moon Crystal was destroyed. Neo-Queen Serenity and Small Lady transformed back into Sailor Moon and Rini. As soon as the Dark Moon Crystal shattered, the quartz encasing Neo-Queen Serenity also shattered and she awoke from her dormancy.
Small Lady returned to Crystal Tokyo, where she was greeted by Mom, Dad, and the Senshi. Crystal Tokyo was beautiful and peaceful once again.
Not long after though, Neo-Queen Serenity realized it was time for Small Lady to be more mature. (She was a spoiled and whiny child, much like her mother!) Neo-Queen Serenity gave Small Lady the first brooch Sailor Moon used (Moon Prism Power, make up!) and a small rod (Pink Sugar Heart Attack!) and then sent Small Lady to the past again, this time to train as Sailor Senshi, Sailor Chibi Moon. When Small Lady returned, she was finally a full-fledged Sailor Senshi, Super Sailor Chibi Moon.
Crystal Tokyo flourished and remained beautiful. The Queen, King, Small Lady, and the Sailor Senshi lived happily ever after.
Manga: Crystal Tokyo has a few differences that are important to point out. The first is that
King Endymion mentions why he and Neo-Queen Serenity do not look old. During the Silver Millenium, the lifetime of people was about a thousand years because the Silver Crystal stopped the aging process when a person reached maturity. When Neo-Queen Serenity became Queen at 22, this same power affected her and everyone in Crystal Tokyo, granting them all long lifespans.
The people of the Black Moon (Dark Moon in the anime) were not from a rogue moon, like in the anime. Nemesis was the tenth planet of the Solar System and it was nicknamed the Planet of Darkness. When they attacked, there was one sudden explosion that wiped out everyone on the planet. Neo-Queen Serenity's body was encased in protective crystal, but not by the Inner Senshi. Her body was encased out of nowhere. Everyone died, including the Inner Senshi, Luna and Artemis. The King was in a deep coma. Only Rini and Diana were unaffected.
Also, in the manga, Chibiusa (Rini) always knew where the Silver Crystal of the future was. She had it around her neck on a necklace with the Time Key. The reason why the Dark Moon wanted to capture her was to get the Silver Crystal, "this stone of illusions that would destroy us".