S-2 most likely refers to a rumored clandestine installation first revealed by former AFOSI Special Agent Richard Doty.

In a probably unrelated note, Site-II was also the original designation for the facility at Groom lake (Area 51).

S-2 Papoose Lake edit

According to Doty, a series of buried trenches and tunnels provide access from the southern end of Groom lake to Papoose lake.

In addition to S-4 at Papoose lake, which Doty alleges was used to house NHI spacecraft, S-2 was a similarly hidden facility designed to study the associated biological entities.