You battle him in lavender town where he as in the graveyard building(forgot actual name) and he asks you why you're there without dead Pokemon and offers to faint them for you. Though he never mentions the reason why he's there. Previously when you fought him on the ship you faint his raticate and there's no Pokemon center on board so his raticate could have died. Is he there to mourn on the death of his raticate?
Im not sure if this is true or not but this article seems legit so read the first part and that might be your answer