I think this might be a Calypso situation. The girl is some kind of supernatural being native to the island who is capable of manipulating their memories so as to never question her presence or her suggestions, such as keeping quiet about seeing boats. Her goal is to keep them on the island, either for food or for pleasure, and she slowly killed off the people who treated her poorly.
When the MC nearly died, he remained some of his memories. He probably realized the truth about the girl at the end but is powerless to do anything about it.