First run by the Army, then the USDA, and now the Department of Homeland Security, Plum Island is the premiere center for "Agroterrorism Defense". As a BioSafety Level 3 facility, the island researches animal diseases such as swine flu and foot-and-mouth disease.
Its future, however is up in the air. The facilities are aging (50 years and counting), and some research requires facilities the Island doesn't have. BSE (or "Mad Cow Disease") requires a BSL-4 lab. There is money in the defense budget for a "National Bio- and Agro-Defense Facility" (which would include a BSL-4), but there's no guarantee that it will be sited at Plum Island. In fact, thet possibility seems remote to many, with the multimillion dollar estates of the Hamptons close by. Some local politicians (Hillary Clinton among them) are fighting for it to remain open, and for a BSL-4 to be built elsewhere.