The Master Crystal is a huge crystal that was found by Doctor Neo Cortex from a cave where he fell to after his last encounter and failed battle with Crash Bandicoot on his zeppelin outside Cortex Castle on Cortex Island.
Cortex brought it back to the new Cortex Vortex, a space station of Doctor Cortex's design equipped with the Cortex Vortex ray cannon, but he still needed 25 more Slave Crystals to harvest the Master Crystal's energy. He planned to use it's power to transform the entire population of Earth into mindless slaves of Cortex.
After the Cortex Vortex was destroyed, it is not seen or mentioned again in the game. It has not been mentioned or seen since and as such it was probably destroyed during the impact of the Cortex Vortex which later accidentally set free the evil Uka Uka from his ancient temple prison.