First came containers loaded with equipment for a secluded property under renovation on the edge of the forest. It had housed a horseback riding academy and a cafe, but was being reconfigured for a mysterious enterprise.

Then muscular young men appeared, jogging through the trees at strange hours and speaking to one another in English.

Juozas Banevicius, who watched the comings and goings in the tiny settlement of Antaviliai, Lithuania, nearly 20 years ago, recalled thinking it a bit odd that the newcomers would shoo away anyone who came close to the security fence they had put up around their property, which was previously open to the public.

“Nobody knew what they were doing inside,” recalled Mr. Banevicius, 66.

The answer has been subjected to intense news media and judicial scrutiny in the years since. It has all pointed to the same conclusion: The village of Antaviliai was home to a secret C.I.A. detention and torture center, one of three so-called black sites that the agency set up in Eastern Europe after the Sept. 11, 2001, attacks.

In January, the European Court of Human Rights ruled that a secret prison code-named Site Violet had “beyond reasonable doubt” been located in Lithuania. It did not name Antaviliai, which is near the capital, Vilnius, but the village is the only place in the country that Lithuanian officials have acknowledged as a site of a former C.I.A. facility — although they insist it was not a prison.