You didn't answer what the lease said about adding occupants. But here's the thing. If he moves out you don't have to. That's the cure.

If he doesn't move out then the landlord goes to court for an eviction order. This will require a hearing. At the hearing you provide proof of how log he has lived there and that the landlord was aware he has been there for 3 years. then its up to the judge to decide whether the landlord ceded her right to object by inaction.