There were hints to Necron in the game. Granted nothing huge but they were there.

Necron though didn't desire to bring an end to everything, it was his purpose. Necron was a being that existed to end life, and was death more or less. It realized that everything had to die and believed one day that a signal would come giving it the O.K. to destroy the crystal and bring everything back to nothing. Necron was just following what it believed it's existence was for, nothing more then the natural force of death at work.