The headquarters is the name often used for the secret meeting place or workshop for The Three Investigators. It was "outdoors, except for a roof about six feet wide, that ran around most of the fence on the inside of the yard". No person could see the three members of the detective firm from the junkyard, where the office was.
Jupiter had arranged piles of various types of junk in the yard, so that the workshop can be hidden, expecially from his aunt, Mathilda Jones, who would assign work to any boy she saw. With the "wall of junk" hiding his workshop, the firm could have privacy when not needed by Jupiter's aunt and/or uncle.