What does that mean? How can he rule if there are no people over whom to rule??
Says Rav Kook in his siddur: ככלות in this context means כיסופין. To deeply desire, to yearn for. After we all properly pine for Hashem then הוא לבדו ימלוך נורא - He will rule alone and there will be no other reality other than us basking in His glory. [See Nefesh Hachaim Shaar gimmel perek yud aleph in the footnote.]
[We need someone to write a really good commentary on the siddur so that people daven with more understanding and emotion. Just an idea if you can do it...]