How to rotate the character controller?

I tried this:

function Start () {
gameObject.transform.Rotate(90,0,0);
}

Everything inside of the character controller rotates, but the movement controls and collider stay the same as if they are not rotated at all. How do I rotate them? I’m trying to make a prone script.

The standard MouseLook-Script does it using this:

transform.localEulerAngles = new Vector3(90, 0, 0);