Lighthouse

"You think the Lighthouse is a prison? Sweetheart... prison would be nice."

- Deke to Daisy Johnson

The Lighthouse is a massive bunker located in a post-apocalyptic chunk of the Earth's crust. It is overruled by the Kree Watch, specifically Kasius and contains a society of subjugated Humans and Inhumans. After being mysteriously teleported there by the White Monolith, Phil Coulson and his team inhabited the Lighthouse.

Early History
The Lighthouse was built as a bunker in the event of an apocalyptic event. During the destruction of the Earth, a large group of Humans survived in the bunker, but were soon enslaved by a group of Kree.

Enslaved Society
The Kree Watch would assert their rule over humanity by forcing them to wear Metrics, a mechanical device that tracked their movements and forced them to comply. Among those enslaved was a man named Virgil who believed in a prophecy telling of a group of S.H.I.E.L.D. Agents who would liberate the inhabitants of the Lighthouse and save the world.

One popular place for the inhabitants of The Lighthouse is the Exchange, a place popular for trading and gathering among the civilians.

Infestation of Roaches
A group of Vrellnexians managed to break into the third level of the Lighthouse from the surface of the Earth. Ever since, the Kree have sealed it off from the rest of the Lighthouse. The Vrellnexians managed to kill everyone who enters the restricted area.

Arrival of S.H.I.E.L.D.
After being captured by a mysterious man, Phil Coulson and his team were teleported through a White Monolith to the Lighthouse. In the Lighthouse, Coulson first meets Virgil, an inhabitant who easily recognises him and tells that he has come to save the humanity before getting knocked out by Alphonso Mackenzie. Coulson and Mack reunite with the rest of the team and Virgil surprisingly recognises all of them moments before he is killed off by a Vrellnexian.

Trivia

 * In the comics, the Lighthouse is an orbital space station built by Hank Pym and Henry McCoy and the headquarters of the Secret Avengers.