Lyric discussion by Somerandomspec 

Cover art for Lost Not Forgotten lyrics by Dream Theater

I think this song is about Mike Portnoy (former drummer for Dream Theater) leaving the band. " I am not immortal I am just a man A power-craving tyrant Beyond the shadows in the sand"

In that way describing his personality.

"Leading the empire Brutal and heartless

thus meaning that he is one of the founding members of the band and that they lost a big part of the band when he left.

They do use the whole 'pharoah' metaphor to describe Portnoy as a king. read the following:

"Behold the kingdom I possess Land of wealth and beauty Where the streets are paved with gold"

He was treated like a 'king' when he was still in the band.

"Vanishing further Into the darkness.." Lost not forgotten King of the deathless soul" meaning he will always be in the band members and fans' hearts.