Eventually, the people of Atlantis began to program their own crystals. Like most humans, the Atlanteans had their own dark desires, causing the crystals to be tainted and consequentially generated psychological problems for both the people who created them, and the people who used them. These crystals inadvertently stimulated dormant brain cells, awakening impulses associated with animal consciousness. Many of those crystals were deliberately programmed to harm others. Soon, an evil spawn of people began to create crystals that didn't contain beautiful notes or colors and instead had discordant notes that damaged the nervous system, and astral colors that aroused the lower passions, such as black, brown, and a a deep purple that was nearly black. Because of those crystals millions died, and many more suffered from a variety of ailments, such as strokes and heart attacks, psychological imbalance, and catastrophic accidents.

The misuse of the crystals is what inevitably led to the destruction of Atlantis. The loss of control over the crystals caused volcanic eruptions, mountains to melt, and possibly altered the axis of the earth slightly.