You can’t cast Clear the Stage without a target creature to get -3/-3. If either target is illegal when Clear the Stage tries to resolve, the other is still affected as appropriate.

You may always choose a target creature card in your graveyard, even if you don’t control a creature with power 4 or greater. Whether you return the creature card is determined only as Clear the Stage resolves.

You check whether you control a creature with power 4 or greater after the target creature gets -3/-3 but before it dies, if appropriate.