It only appeared in the 1st season of the original anime and was used by three separate members of the Dark Kingdom, each with a different purpose.
After repeated failures, Nephrite decided to search for the Silver Crystal on his own, despite the fact that this was Zoisite's job. He went to his secluded secret mansion and consulted the stars, asking for a guide to finding the Silver Crystal. Using the powers of the stars and of himself, he created the Black Crystal, which immediately began to glow and show an illusionary image of Naru. Of course, this led Nephrite to believe that Naru had the Silver Crystal. He quickly learned that the Black Crystal was responding to Naru's love for him and that she did not really have the Silver Crystal. Zoisite managed to have Nephrite killed in episode 024 in order to steal the Black Crystal from him.
In Episode 25, Queen Beryl revealed the history of the Silver Crystal, saying that long ago, it was split into seven Rainbow Crystals by Queen Serenity herself in order to seal away the Seven Great Youma. In order to recreate the Silver Crystal, the seven Rainbow Crystals had to be found inside of the seven humans who are reincarnated youma. Queen Beryl modified the Black Crystal so that it would respond only to Rainbow Crystals, then gave it back to Zoisite. He was then able to use the crystal to locate the seven Rainbow Crystals carriers and extract the Rainbow Crystals from their bodies. After the seven crystals were extracted, a battle ensued in which the Sailor Senshi, Dark Kingdom, and Tuxedo Mask all fought for control of them.
In episode 32, the Black Crystal underwent another transformation. This time, Zoisite immersed it in a potion which enabled him to use the crystal to transform ordinary humans into youma. He intended to use the crystal to transform Naru into a youma and lure Sailor Moon out into the open, in an attempt to get back the yellow Rainbow Crystal. He accidentally missed his target and transformed an actor in the Redman show into the youma Akan.
After the seven Rainbow Crystals were gathered in one place and formed the Silver Crystal from Sailor Moon's tear, the Black Crystal was not seen again until episode 41. Prince Endymion, who had been brainwashed and was working with the Dark Kingdom, was attempting to capture all seven former Rainbow Crystals carriers and trap them within the Black Crystal. The Dark Kingdom hoped that although the former youma had been healed by Sailor Moon, they would be able to use their energy and the power of the Black Crystal to transform them back into youma. After they were reunited, it was hoped that they would come together to form one extremely powerful youma to destroy the Sailor Senshi. Sailor Mercury was ultimately able to take the crystal from Endymion and throw it to the ground, shattering it and freeing the six former Rainbow Crystals carriers who had been captured.