It is a story wherein Cloud goes back in time because the planet is literally dying (black things are stripping away the life of the earth). There are kind of wolf dynamics of alpha, beta, and gamma. Before Cloud is sent back, he is asked to say "Kneel," which everyone blissfully responds to. During this state, the people are extremely malleable.
So in this universe, people are separated into alpha, beta, gamma, and so on all the way to omega classifications. It also occurs in SOLDIER. Cloud while as a cadet using codes given to him steals information, and commands people to follow his instructions and then "stop breathing." When he faces off against Sephiroth and Angeal, he says, "On your knees, Sephiroth" three times. Cloud has this power because he is the Ultima.
When he saves Vincent, he knows that beta Vincent has to be physically restrained instead of verbally ordered. After the destruction of Shinra and Jenova, Cloud promises to become only Vincent's Ultima. (There is d/s undertones of bondage for Vincent, and a slight hint of Cloud/Vincent.)
Please help me! Thank you!