Most antihero stories feature the antihero as the protagonist though, and they tend to be the lesser evil among many morally bad characters. I can't think of many examples of the antihero trope where they coexist with a "good" protagonist and the protagonist ends up siding with the antihero. Usually it's the complete opposite, something like RRR or the shounen cycle where an antihero character who starts off as a powerful villain becomes an ally to the unambiguously good protagonist when faced with a common enemy.