In the framework of Project Reclamation, S.H.I.E.L.D. officer and General Rick Stoner spearheaded the creation of the secret facility which would be known as the Lighthouse. This underground facility was located beneath a real lighthouse on a small cliff on Lake Ontario, near the city of River's End. Despite the Lighthouse being underground, Stoner managed to grant access to aircrafts: a small part of Lake Ontario could be emptied, giving the aircrafts access to a landing bay.
When the Hydrogen Wave Crisis was solved, the Lighthouse was abandoned and no one knew about the secret Lake Ontario facility any longer. Years later however, the Inhuman Robin Hinton guided the Chronicom Enoch to the facility. Enoch in turn informed his fellow Chronicom Noah about the place and both the Chronicoms settled in Lake Ontario to monitor Earth activities. Enoch later took Leo Fitz, Lance Hunter, Polly Hinton and Robin to Lake Ontario so they would be safe from General Hale.
Upon returning into their time, S.H.I.E.L.D. made the Lake Ontario facility their primary base of operations. Daisy Johnson discovered the secret underwater landing bay and opened it when her teammates returned from the St. Louis Aerospace Facility with the massive Zephyr One. Later, Deathlok also brought a Quinjet full of S.H.I.E.L.D. agents beneath the lake's surface.
The S.H.I.E.L.D.'s Zephyr One briefly left Lake Ontario while they were searching for Gravitonium and when they attempted to capture General Hale.. Melinda May returned the Zephyr One to Lake Ontario and informed her colleagues of Phil Coulson's capture, so Quake and May left to find Robin while Yo-Yo Rodriguez, Leo Fitz and Jemma Simmons later left Lake Ontario with a Quinjet. With Robin's assistance, Quake and May successfully rescued Coulson and Glenn Talbot and returned the Zephyr One to Lake Ontario. They left again for an Attack on the HYDRA Preparatory Academy and returned to Lake Ontario following the Infiltration into the HYDRA Herefordshire Facility.
In an attempt to reclaim the Gravitonium from S.H.I.E.L.D., Qovas took his spaceship over the shores of Lake Ontario and laid siege on the Lighthouse. However, his attack failed due to Talbot who infused himself with the Gravitonium, killed the Remorath soldier and flew himself and Coulson on a concrete chunk to infiltrate Qovas' spaceship, who remained over the lake. The Zephyr One later left Lake Ontario to join the spaceship who had left for space, and returned following the destruction of the Remorath spacecraft.
In chronological order:
- Agents of S.H.I.E.L.D.
- Season Five
- Season Six
In an alternate timeline:
- ↑ 1.0 1.1 Agents of S.H.I.E.L.D.: 5.11: All the Comforts of Home
- ↑ Agents of S.H.I.E.L.D.: 5.05: Rewind
- ↑ Agents of S.H.I.E.L.D.: 5.12: The Real Deal
- ↑ Agents of S.H.I.E.L.D.: 5.13: Principia
- ↑ Agents of S.H.I.E.L.D.: 5.14: The Devil Complex
- ↑ Agents of S.H.I.E.L.D.: 5.15: Rise and Shine
- ↑ Agents of S.H.I.E.L.D.: 5.16: Inside Voices
- ↑ Agents of S.H.I.E.L.D.: 5.17: The Honeymoon
- ↑ Agents of S.H.I.E.L.D.: 5.18: All Roads Lead...
- ↑ Agents of S.H.I.E.L.D.: 5.19: Option Two
- ↑ Agents of S.H.I.E.L.D.: 5.20: The One Who Will Save Us All
- ↑ Agents of S.H.I.E.L.D.: 5.21: The Force of Gravity
- ↑ Agents of S.H.I.E.L.D.: 5.22: The End