Here is the apology that would be acceptable from the Vatican:
Sell all of their assets.
Distribute the proceeds among all victims of clerical sex abuse.
Hand over all clergy involved, in any way, in said abuse, whether in committing it, covering it up, or engaging in victim-blaming.
Shut down operations and cease to be a blight on humanity.
EDIT: And apologize for the incredibly evil teaching of Hell, which has probably been responsible for more nightmares (at least of things that aren't real) than anything else in the history of humanity.