The Cyan Crystal is a powerful object that is the source of a skillset known as Cyan. Users of Cyan have the ability to heal, fortify structures, and even bring people back from death (in exchange for another life). It was used by the Unknown Guild on Magna Iun before it was taken by Turaga Niici to Terros Nui. Its primary use was as a power source for the research facility.
It was later revealed that this crystal and the Sapphire Crystal had to be merged in order to set a balance to the overwhelming power. The result was Zyklonn's freedom from the time warp. Grateful, he volunteered to help Likeron and his friends on their quest. Zyklonn is a Xa-Kuta Master who was imprisoned by Insontro and studied by a black Toa of Ice named Aqi. Zyklonn was put into stasis and his essence was split into two crystals. Thus, the Cyan and Sapphire Crystals were actually extensions of the Xa-Kuta power.