The Brave New World tricks John by letting him believe he is free to come and go in society as he pleases. However, when he wants to go to the free islands with his friends Bernard and Helmholtz, Mustafa Mond refuses telling him that the "experiment" isn't over.
John is not a welcome guest, but an experimental rat being moved about by the leaders to study what happens when an unconditioned person enters into the conditioned world.
He is allowed to go by himself to the lighthouse to live out his days (or so he thinks). The media is allowed to find him and make movies about him so the rest of society shows up to harass him.
In short, the Brave New World drove John to his death by forcing the dystopia on him.