Bakes animation to the skeleton (joint objects) and disables the Control Rig (if your character has one.) Select this option, for example, when you are finished adjusting the retargeted animation.
You can also select Bake To Skeleton > 
to open the Plot Selected Properties window. See Plot Properties window.
Bakes animation to the Control Rig objects. The Control Rig objects receive one keyframe for each frame of the current character's animation.
Select this option if you want to continue adjusting the retargeted animation, but you no longer need the source character in your scene.
You can also select Bake To Control Rig > to open the Plot Character Properties window.