The Astonishing is an analogy of how JP, JLB, JM and JR started a rebellion to get free of Portnoy's ironfist tyrannical rule.
So, the entire album is a sequel to Outcry, it wasn't Metropolis PT3, but Outcry PT2
"We suffered far too long... We gather now... Growing stronger... We will not be ignored, anymore, any longer..."
See?