Today the facility maintains laboratories up to biosafety level 3, and has remained controversial as a result of its high-risk work and proximity to the New York metropolitan area.

[5] Local Long Island activists prevented the center from expanding to include diseases that affect humans in 2000, which would require a Biosafety Level 4 designation; in 2002, the US Congress again considered the plan.

[4] The Wall Street Journal reported in January 2002 that many scientists and government officials wanted the lab to close, believing that the threat of foot-and-mouth disease was so remote that the center did not merit its $16.5 million annual budget.

[7] In 2020, the Department of Homeland Security plan to put the island up for auction after the conclusion of laboratory activities in 2023 was blocked by Congress.

As part of ongoing COVID-19 pandemic relief legislation, Senator Chuck Schumer of New York negotiated a provision in the CARES Act that protects the island from being sold.

After the final draft of the legislation was announced, Schumer said “It would have been a grave mistake to sell and develop Plum Island's 840-acres of habitat, which is home to many endangered species, that's why preventing the unnecessary sale requirement was a top priority of these negotiations.

"[8] On September 11, 2005, DHS announced that the Plum Island Animal Disease Research Center will be replaced by a new federal facility.

The location of the new high-security animal disease lab, called the National Bio and Agro-Defense Facility (NBAF), is being built in Manhattan, Kansas.

[17] The USDA facility, known as the Plum Island Animal Disease Center, continued work on biological warfare research until the U.S. program was ended by Richard Nixon in 1969.

[18][19] The existence of biological warfare experiments on Plum Island during the Cold War era was denied for decades by the U.S. government.

In 1993 Newsday unearthed documents proving otherwise and in 1994, Russian scientists inspected the Plum Island research facility to verify that these experiments had indeed ended.

Foot-and-mouth disease was eradicated from the U.S. in 1929 (with the exception of the stocks within the Plum Island center)[4] but is currently endemic to many parts of the world.

[7][10] In response to the two 2004 incidents, New York Senator Hillary Clinton and Congressman Tim Bishop wrote a letter to the Department of Homeland Security regarding their concerns about the center's safety: "We urge you to immediately investigate these alarming breaches at the highest levels, and to keep us apprised of all developments.

[22] Fort Terry went through a period of activations and deactivations through World War II until the U.S. Army Chemical Corps took over the facility in 1952 for use in anti-animal biological warfare (BW) research.

[22] Fort Terry was officially transferred to the USDA on July 1, 1954, at the time scientists from the Bureau of Animal Industry were already working in Building 257.

[17] Construction on Plum Island's new laboratory Building 101 began around July 1, 1954, around the same time that the Army's anti-animal bio-warfare (BW) facilities at Fort Terry were transferred to the U.S. Department of Agriculture.

[24] Prior to the building's opening the area around it was sprayed with chemicals to deter insect or animal life from approaching the facility.

[25] A discredited 2004 book entitled Lab 257: The Disturbing Story of the Government's Secret Plum Island Germ Laboratory fueled the conspiracy theories.

The creature, a quadruped of indeterminate size, was dead when discovered, and was assumed by some to have come from Plum Island as a result of the currents and proximity to the mainland.

[28] When American educated Pakistani neuroscientist Aafia Siddiqui, a suspected al-Qaeda member, was captured in Afghanistan in July 2008, she had in her handbag handwritten notes referring to a "mass casualty attack" that listed various U.S. locations, including the Plum Island Animal Disease Center.