The US Military used underground bases, chambers, rooms & tunnels around St Thomas to protect the submarine base. Later they were repurposed for Agent Orange (which was designed to be used against enemy humans) weapons testing "on doves and goats" in what just happens to be the poorest, most remote African-American location under United States control.
Maybe the DoD built an underground bunker, base, fort under Little St. James as it did on other St. Thomas islands such as nearby Water Island or the main island of St Thomas in WWII.
On Water Island, the underground rooms and chambers were used for chemical weapons testing using a precursor to Agent Orange "on goats and pigeons" after WWII.
You do realize the government didn't locate a secret, underground chemical and biological weapons testing base next to St Thomas because of its ample supply of goats and pigeons, right? Seems more likely it is because it has an ample supply of humans who nobody would miss, doesn't it?
What are the odds after they closed and abandoned the Water Island chemical and biological weapons testing base because it was too close to the main city, that they built another just a little farther out of view? Only to abandon a hypothetical Little St James base later?
If there was a second round of underground bases, were they run by the military or the CIA? Inextinguishable supply of humans to test weapons on?
Could Epstein have simply refurbished and updated an abandoned base? Couldn't Epstein have used Lifeboat Foundation LifeShield Bunkers to do the refurbishment? This could explain the lower scale of construction uncovered so far, couldn't it?
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"Fort Segarra - Water Island, Virgin Islands"
https://m.youtube.com/watch?v=aLqb6whByt4
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Life Magazine printed an article about the underground fort on Water Island on January 12, 1962 in an edition about doomsday bunkers.
https://www.goantiques.com/life-magazine-jan-47329203
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"History of Water Island In The U.S. Virgin Islands"
http://www.waterislandhistory.com/militaryhistory.html
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"Most travelers have never heard of this gorgeous US island in the Caribbean"
https://www.businessinsider.com/water-island-is-a-secret-island-in-the-usvi-2015-7
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"These 12 Formerly Top-Secret Bunkers Are Now Tourist Attractions"
https://www.fodors.com/news/photos/these-12-formerly-top-secret-bunkers-are-now-tourist-attractions
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Fort Segarra, Water Island, St Thomas, Virgin Islands (can see the island from Little St James)
https://en.wikipedia.org/wiki/Water_Island,_U.S._Virgin_Islands
"Fort Segarra was built as part of the United States' defense strategies during World War II on Water Island in the U.S. Virgin Islands in the Caribbean. World War II seacoast batteries here were Battery 314 at Flamingo Point (1944, never completed) and an Anti Motor Torpedo Boat Batteries. In addition, some barracks, watch towers, AMMUNITION BUNKERS were also created near Carolina Point as well as an infrastructure of docks, roads, water, sewage and POWER SYSTEMS. It was to be an UNDERGROUND FORT and its purpose was to protect the submarine base on St. Thomas. The war ended before its completion and the project was subsequently ABANDONED. The uncompleted post was transferred to the Army's Chemical Warfare Division in 1948 for testing poison gas and chemical agents on goats and pigeons for several years. Following the conclusion of these tests, the Army transferred control of this area to the Interior Department in 1952.
Gun emplacements, TUNNELS and UNDERGROUND ROOMS which were created during the World War II building efforts are still visible. The site is now open for viewing, and TUNNELS and UNDERGROUND CHAMBERS are open for tours. The area is monitored by the United States Army Corps of Engineers and soil samples are monitored from the former chemical test sites to ensure "that no residual contamination remains from previous Department of Defense activities.""