Sanctuary Fortress was the first area on Aether settled by the Luminoth, founded by E-Btr at the beginning of their Golden Age. Home to several of their most technologically advanced achievements, Sanctuary Fortress proved to be a safe haven following the catastrohpic meteor impact that heralded the Luminoth Dark Age, protected from the Ing by various Mechanoids built by Luminoth inventors. The Portals that appeared in Sanctuary led to the Ing Hive, the very heart of the Ing Horde, where many battles were waged. C-Pul, a great hero of Sanctuary known as the Ingslayer, eventually fell in one such conflict, the Battle of the Hive.
Gradually, the mechanoid sentinels were turned against their Luminoth creators and used by the Ing for their own purposes. O-Lir, the last Sentinel of the Sanctuary Temple, was eventually slain by his own creations, and Sanctuary fell. What Luminoth remained retreated to the Great Temple.
Nearly all enemies Samus encounters here are mechanoids built by the Luminoth to combat the Ing which have since turned against their creators, the most common of which are Quads and Rezbits. Others encountered include Ingsmashers, the Caretaker Class Drone, Diligence Class Drones, Luminoth Turrets, Mechlops, Mekenobites, Octopedes, and the mighty Quadraxis.
When Samus first goes to Sanctuary, she is ambushed by a large group of Pirate Commandos. She also encounters Dark Samus twice in Sanctuary. The first time was shortly after Samus recovered her Spider Ball. While Samus travels back to Torvus Bog, Dark Samus destroys the bridge across the Sanctuary Entrance in an attempt to trap Samus. She later battles Dark Samus in the Aerie.
- "This is a statue of E-Btr, the founder of Sanctuary. He lived for nearly 5 centicycles, and died in hand-to-hand combat during the first Ing attacks." —Scan Data (Metroid Prime 2: Echoes)
- "Aether was a fertile, aged world with bountiful fields and oceans. The native creatures were gentle compared to other worlds we had encountered. We settled in a mountain region at first, in cliffside dwellings. In time, we established settlements in the green forests of Torvus and the fertile plains of Agon. A Great Temple was built between our three domains, a place of peace and a monument to our accomplishments. It was a time of harmony for our people." —Luminoth Lore (Metroid Prime 2: Echoes)
- "This used to be a great fortress, a safe haven for our people during the war. It also holds portals to the Ing Hive, the heart of their dark tribe. During the war, I built a number of mechanical sentinels to join me in battle. They were made to fight the Ing, and fight them they did...for a time." —O-Lir (Metroid Prime 2: Echoes)
- "One by one, the Ing corrupted them. Now, they attack with no mercy. Many went to Dark Aether with their Ing masters. Expect them when you are in the Hive. The Ing like to use them as guards. The Ing will protect their home with great ferocity. In all of our battles, the Hive has never fallen." —O-Lir (Metroid Prime 2: Echoes)
- "This is a statue of C-Pul, a great hero of Sanctuary. Known as the Ingslayer, C-Pul defeated over 700 Ing in combat before his death in the Battle of the Hive." —Scan Data (Metroid Prime 2: Echoes)
- "Bioscan complete. Luminoth subject terminated 1.1 decacycles ago. Subject has taken damage from a number of Luminoth weapon systems, most likely those used by rogue Luminoth combat drones. It took more than the Ing to defeat this warrior." —O-Lir (Metroid Prime 2: Echoes)
- "Our battered forces gathered in the Sanctuary Fortress to prepare for the inevitable siege there. They didn't wait long. Wave after wave of Ing assaulted the greatest of our fortresses, with one goal in mind: to seize the energy there. The Ing turned the machines of Sanctuary against our warriors, and soon all was lost. The energy of Sanctuary was taken by the Ing. Only one Energy Controller remained on Aether." —Luminoth Lore "Sanctuary Falls" (Metroid Prime 2: Echoes)