The Gormogon Vault is a secret underground shrine to the Gormogon Order that was originally cut into the foundation of an abandoned bank called Capital Mutual Bank on the Anacostia River which was in the process of being re-preserved as a historical site by the DC Building Conservatory. The entire Vault was moved to the basement of the Jeffersonian Institute, by the request of Dr. Temperance Brennan, so that it's contents could be cataloged and studied. The Gormogon Vault is still currently in the basement of the Jeffersonian Institution.
The Vault appears to contain the largest collection of Gormogon artifacts in the world. The Vault holds museum quality tapestries, paintings, books, weapons, and other artifacts related to the victims of the Gormogons as well as a number of mystical orders and traditions:
Bones: Dead Languages. Egyptian Art. Pythagorean Mathematics. Hebrew Scriptures. Gnosticism. Kabala. Alchemy. Druidism. Astrology.
The key feature of the Vault was a Silver Skeleton arranged in a unique pose known as "Pharmakos", a position, according to Hodgins, which was known to the ancient Greeks as one of sacrifice, rapture, or the symbolism of a scapegoat. For the Freemasons, the position is known as "The Widow's Son." The Vault also yielded a tapestry whose pattern corresponds to specific locations in Washington, D.C. and to tarot cards showing different archetypes, such as the Musician (Gavin Nichols), the Bishop (Father Cooper), and The Corrupter (Ray Porter). An ancient Greek inscription was burned on the back of the Vault's door. It translated to "Will no one help the Widow's Son?"
Gormogon placed a few hidden devices into the Vault to discover if someone broke into the Vault. A transmitter that would activate when the Vault door was opened and a sensor that takes audio and video behind a stone sculpture representing the All-Seeing Eye that would activate whenever someone turns on the lights. A bunch of mirrors were placed all around the Vault to allow the sensor to take video of every corner of the Vault. This security system allowed Gormogon to keep track of everything that happens in the Vault at all times.
Gormogon's goal was to re-assemble the Silver Skeleton of the Widow's Son into a replica made from human bones. The specific bones from each specific victim symbolized the victim's position which reflects the figures on the tarot cards sewn onto the Tapestry. After they first found the Silver Skeleton, they deduced that the bones on it came from 7 victims so far. Gormogon was performing the ritual by targeting people representing the tarot card figures in order: the targeted archetypes included the Architect, the Martyr, the Orator, the Musician, the Bishop, and the Corrupter. All the victims took a trip to the Anatolia Region in Turkey where it was believed to hold the legendary site of the Garden of Eden. When he apprenticed Gormogon, Arthur Graves was able to create a replica of the Widow's Son Sculpture from human bones from over 30 victims and concealed it in a mausoleum in Silver Hill Cemetery. In The Knight on the Grid, Gormogon sent Father Cooper's patellas to Brennan to add them to the Silver Skeleton. After realizing that Gormogon was watching them, Brennan added the patellas on the Silver Skeleton because she and Booth had a plan to lure Gormogon out of hiding by making him believe that they were taking the Silver Skeleton to an MRI in Bethesda. Gormogon detonated a bomb using his own teeth as shrapnel to try to kill Booth and Brennan because they knew that he was going after Ray Porter. After he was saved by Booth, Ray Porter was eventually killed by The Apprentice in his home. In The Pain in the Heart, Gormogon sent Ray Porter's mandible to the Jeffersonian along with a pair of silver screws to get them to add it to the Silver Skeleton. When Zack Addy caused an explosion that tore his hands apart, it gave Gormogon enough time to sneak into the Jeffersonian to steal the Silver Skeleton. After searching through Limbo, many of the interns at the Jeffersonian located the rest of Ray Porter's bones which were scattered throughout the bone drawers and they also realized that many of the skulls in the drawers were missing their canine teeth. Brennan realized that Zack was working with Gormogon while examining the mandible and realizing that he made Gormogon a set of dentures with nothing but canines which were associated with the wolf. The wolf appeared on the Tapestry as a symbol of freedom representing the forces that deliver from persecution. After Brennan refuted his logic and emphasized how he risked everything to avoid hurting Hodgins, Zack disclosed the location of Gormogon's house in Benning Ridge on Savoy Crescent Street. The Silver Skeleton can be seen at Gormogon's house across the chamber where Gormogon was eating human flesh before he was shot and killed by Booth and his SWAT team.
When she was kidnapped in The Nightmare within the Nightmare, Brennan was greeted by Zack for the first time in eight years in the Vault. The Silver Skeleton was later seen whole in The Hope in the Horror when Booth was looking for Brennan and Zack in the Gormogon Vault. It can be assumed that when the Silver Skeleton was reclaimed and returned to the Jeffersonian, they searched Gormogon's entire house for more evidence and, in the process, discovered the pieces of the Silver Skeleton which were removed when Gormogon was replacing the pieces with actual human bones. They would have added them to the Silver Skeleton while the human bones were preserved as evidence in the murders of the people from whence they came.
In The Steal in the Wheels, Hodgins moves the contents of the Vault to his office as part of his attempt to find evidence exonerating Zack Addy. With the help of Doctor Gordon Wyatt, Hodgins is able to use the historical records from the Vault to help him locate the body of The Apprentice, Ray Porter's true killer, who was buried beneath an Acacia Tree on the west side of the original boundary lines of Washington D.C. in an inverted Masonic Coffin made of stone. They were able to use their newfound evidence exonerate Zack from the murder charge and the life sentence in The Day in the Life. When the Jeffersonian was detonated, it can be assumed that the Vault survived the explosion since the entire building never came crumbling down after Booth was able to deactivate one of the bombs. As of The End in the End, the Jeffersonian is currently undergoing reparations and renovations and the Vault is still intact.
☀ The name of the bank; Capital Mutual Bank, was used in The Goop on the Girl as the name of the location of the attempted bank robbery in the episode. It can be assumed that when the bank containing the Vault was closed down, the business was relocated to the current location on the intersection on 12th and U Street in Washington D.C. while the original foundation became preserved as a historical site by the DC Building Conservatory.