- "The priest pulls out another skull, crystal, and holds it high. The relic! I hear its hum in my own skull. Faint, but familiar!"
- ―Giovanni Borgia, upon first sighting a Crystal Skull, 1520.[src]
The Crystal Skulls were Pieces of Eden that functioned as communication and observational devices. Created by the First Civilization, three distinct variations of Crystal Skulls have been discovered so far.
The first type functioned much like modern telephone devices, allowing communication between all who possess a device. The second type has a record-and-playback function, allowing a user to record and send audio-visual messages to others who possessed a counterpart Crystal Skull. While the third worked as a monitoring devices, projecting audio-visual surveillance through connection with a living being's blood in a vial.
The Crystal Skulls have notably been found in the remains of the old pre-Columbian civilizations of the Americas.
- "I hear talking, but I cannot understand the words! I see a face within its cloudy core. No... in my mind. It has appeared in my mind!"
- ―Giovanni studying the Skull, 1542.[src]
Returning to Europe with the artifact, Giovanni took it to the scientist Bombastus, who was an expert in studying the Pieces of Eden. Though he subjected it to several tests, Bombastus was unable to discover its purpose, and the Brotherhood dismissed the Skull as little more than an ornate treasure.
Despite this, Giovanni continued to study the Skull, gazing into it for at least an hour each day for about 22 years. Finally, in 1542, an unknown Chinese man, who had also acquired a Skull, used its communicative powers to contact Giovanni.
In 1719, the Sage and pirate Bartholomew Roberts agreed to take Edward Kenway to see the Observatory, a First Civilization complex used to monitor the lives of people whose blood had been collected in blood vials. Central to the Observatory was the viewing device: a large armillary sphere with a Crystal Skull fixed in its core, where the vials would be inserted. The device would then spin and project images onto the wall behind it.
After leading Kenway to the center of the complex, Roberts activated the Crystal Skull that the Observatory housed to take a look through the eyes of Jack Rackham and Woodes Rogers. Betraying Kenway and leaving him locked in the Observatory, Roberts took the Crystal Skull and kept it with him while he sailed the West Indies and West Africa for the next three years.
Kenway later tracked Roberts down to the island of Príncipe, and pursued him along the coast of West Africa before boarding his ship and killing him, taking the Crystal Skull with him. Returning to Havana, Kenway inserted Grand Master Laureano de Torres y Ayala's blood vial into the Crystal Skull to discern his location.
He left the artifact in Rhona Dinsmore's care while he searched for his target, only to discover he assassinated a decoy, with Torres' vial having been purposely mislabeled, presumably to keep his fellow Templars from spying on him. Soon afterwards, the Observatory was found by the Caribbean Templars, and Kenway hurried to stop their endeavor to take the complex for themselves. After killing Torres, Kenway and the Assassin Mentor Ah Tabai placed the Crystal Skull back in its original location and sealed the Observatory, hoping to keep it out of the wrong hands.
The Templars planned to use them as a completely secure means of communication, which the Assassins would be unable to trace. Due to their limited number, only the most essential facilities or members would have access to the Skulls.
- A message that Clay Kaczmarek wrote stated that "Within Emperor Jiajing's sin and Quetzalcoatl's hunger lies the answers." The Chinese man who contacted Giovanni could presumably have been Emperor Jiajing, a Templar-aided Chinese emperor, who hunted the Chinese Assassins. Quetzalcoatl is a reference to the Mesoamerican deity, which would tie to the Mitchell-Hedges Skull.
- It was suggested by the author of an Abstergo memo on various First Civilization artifacts that the shape of the device – a human skull – was the result of a bizarre fashion trend.