The guest house is not a SHIELD Facility. We don’t know who or what’s in there.
The guest house is a non-operational military bunker from 1945, that is “a heavily fortified facility located in a mountain approximately 17 miles northwest of [REDACTED].” It was used as a “munitions bunker during World War II and later upgraded for use as a [REDACTED] by the SSR.”
Landing Site
Coulson, in an effort to discover how he was brought back to life and find a way to save Skye, visits this secret facility. The landing zone and exterior entrance were filmed just south of the Korean Friendship Bell at Angels Gate Park in San Pedro. The entrance is part of the World War II bunkers scattered around this bluff in San Pedro, which are all parts of the former Fort MacArthur.
MAP
Interior Tunnels
Coulson and team breach the facility and run through a number of tunnels to get to the lab where the GH.325 serum is stored. According to Agents of SHIELD Season One Declassified, the tunnel portions were filmed at a “water reclamation plant,” while the lab and further interiors were set up on the soundstage. The Donald C. Tillman Plant in Van Nuys is the best guess for these interiors, with the plant having been used for many film and television productions, as well as the louvered ceiling approximating the metal grating seen in satellite photos.
MAP
(Agents of SHIELD S01E14, 2014)
MCU: Location Scout 