Verified answer

They ruled for him in effect. Theirs was military might- contrary to his "spiritual" right. Whomever guarded or controled the Emperor ran the country- thus leading to the first Shogunate.

daimyos became more powerful and eventually used the Emperor as a figurehead of power, not actual power. I think this occured under Tokugawa Ieayasu. Heian period? don't hold me to that. but i think.