Ezra must apologize__ what he has done.

The phrase "apologize for" is idiomatic in English and follows the grammatical rule that "for" is used to indicate the reason or cause for an action. When apologizing, "for" is used to specify the action or behavior for which the apology is being made. Therefore, in this context, "for" is appropriate because it indicates the reason or cause for Ezra's apology, which is what he has done.