When Agents of S.H.I.E.L.D. season 5 began, it took Coulson and his team to a terrible future in which the world had been destroyed - apparently by one of their own. The last remnant of the human race lived inside the Lighthouse, a mysterious bunker that had actually survived the end of the world. The S.H.I.E.L.D. team has spent most of season 5 trying to learn just what happened to the Earth, but another question has rumbled in the background: Who created the Lighthouse, and why?
In the comics, the Lighthouse was actually an orbital space station, the headquarters of Steve Rogers's Secret Avengers team. The Lighthouse of Agents of S.H.I.E.L.D. has clearly been very different; until now, though, its origin has been shrouded in secrecy. Finally, the latest episode - "All the Comforts of Home" has revealed the Lighthouse's secret origin.
The Secret History of the Lighthouse
The Monolith returned Coulson and his team to their own time, but they were still in the Lighthouse. Even as the S.H.I.E.L.D. team struggled to reorient themselves, they were greeted by a recording from General Stoner. A past Director of S.H.I.E.L.D., it seems Stoner had the Lighthouse built when the Earth faced a near-extinction event. Coulson himself referred to the threat of something called a "Hydrogen Wave" - a crisis that was averted in 1972.
Stoner clearly believed the human race was in danger of extinction. He launched an innovative plan to create a bunker that could actually survive the end of the world. No doubt the project took years, suggesting the threat of this "Hydrogen Wave" was one that loomed over the Earth for quite a while. In the event of cataclysm, Stoner's intention was to assemble the world's best and brightest in the Lighthouse. They would survive the Hydrogen Wave, and then go back to the Earth's surface to reclaim their ravaged world. Stoner referred to this as "Project Reclamation."
According to Coulson, the Lighthouse's existence was lost in the mists of time. For as-yet-unknown reasons, Stoner covered up the Lighthouse project, erasing all records from S.H.I.E.L.D. files. Even Fury's Toolbox, passed on to Coulson when he became Director, didn't contain a reference to the Lighthouse.
Home of the Chronicoms
With the Lighthouse forgotten, it seems the Chronicoms chose to make it their base. They've updated the '70s-era S.H.I.E.L.D. technology, providing it with state-of-the-art computer systems (and possibly beyond). What's more, the Chronicoms have also used the Lighthouse as a place to store some of the most dangerous artifacts on Earth. S.H.I.E.L.D. has already discovered an entire cache of Kree Monoliths, of varying textures and colors. The Chronicoms have clearly interfered to prevent a number of extinction-level events over the decades. The Lighthouse has been their base of operations, and is pretty well-equipped.
"All the Comforts of Home" ends with the death of what seems to be the last of the Chronicoms, the appropriately-named Noah. In the present, the Lighthouse - and everything within it - now belong to the S.H.I.E.L.D. team. They now live in what may be the most secure S.H.I.E.L.D. site on the planet, one which even Nick Fury may well be unaware of. It's the perfect bolt-hole for the "world's most wanted."
Meanwhile, it's testimony to the genius of S.H.I.E.L.D.'s technicians back in the '70s that the Lighthouse actually will survive the end of the world. This bunker is sturdy enough to stay in one piece when the entire planet is Quaked apart; it will ultimately become home to the last remnant of the human race. Even in the twisted, dystopian future Coulson and his team visited, it was S.H.I.E.L.D. who had ensured humanity had a future.