Each of the rainbow crystals, along with the soul of one of the shadows, was kept inside a different person, until they were extracted by Zoycite (though the shadows were killed when Sailor Moon healed the carriers). Zoycite got four crystals, however the Sailor Scouts got one, and Tuxedo Mask got two. Eventually Sailor Moon was forced to hand over her crystal to Zoycite.
Zoycite challenged Tuxedo Mask (Darien) to a battle over the crystals, but had Malachite take all seven of them. However, after Tuxedo Mask was injured by Zoycite, the crystals combined into the Imperium Silver Crystal, transforming Sailor Moon into Princess Serena. She defeated Zoycite with Cosmic Moon Power. Malachite's arc revolved around him trying to find Sailor Moon and take the crystal (as it was needed to release the Negaforce), but eventually Sailor Moon defeated him with Cosmic Moon Power, killing him by reflecting his own attack back at him. Cosmic Moon Power was also used to destroy Queen Beryl (combined with the Negaforce as well) with a massive energy ball.
The silver crystal of the future was taken by Rini, and vanished inside her before she and the Negamoon Family traveled into the past. Though one silver crystal was weaker than the Dark Crystal, Rini discovered her silver crystal while Princess Serena was fighting Wiseman, and with both of them using two silver crystals, they proved to be stronger than the dark crystal, decimating it and destroying Wiseman.