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Their power was used by the scientists at Black Mesa in their research to create a reliable and safe means of teleportation. It was GG-3883, the purest sample to ever be discovered by these scientists, which triggered the infamous Black Mesa Incident.
The Nihilanth was able to regenerate its health by drawing energy from three of these crystals located in its chamber, and the test sample that Gordon Freeman placed in the Anti-mass Spectrometer was made of this same material. Since the device used to analyze the material was an Anti-Mass Spectrometer, Xen crystals must contain a substance that has anti-mass, or in other words, negative mass. Not to be confused with antimatter, negative mass is a property of a theoretical substance known as exotic matter. Scientists have theorized that if exotic matter could be discovered or created it might be possible to open up a Wormhole, a sort of tunnel or shortcut through space or between universes.
It is unsurprising that the Black Mesa scientists had a great interest in Xen crystals – as well as scientific curiosity, there were also obvious technological applications for a natural source of exotic matter. The teleporters developed at Black Mesa were enormous machines that required tremendous power supplies, but if the exotic energy in the Xen crystals could be harnessed teleportation could be made much simpler and more economical. The exotic energy was sometimes referred to as displacement energy due to its usage in the teleportation process. It is likely that the Xen crystals are a mix of both exotic matter and more normal matter, and since the sample that Gordon Freeman handled was "the purest sample yet" it is likely it contained more exotic matter than previously discovered. Unfortunately, such a high concentration of exotic matter meant that the crystalline material had bizarre physical properties and was therefore very unstable. The powerful beam of the overloaded Anti-Mass Spectrometer damaged the crystal’s structure, causing a self-sustaining chain reaction known as a resonance cascade. The resulting release of exotic energy had devastating effects on the fabric of space-time, forming a ‘dimensional rift’ between Earth and the Xen border world.
At the time of the disaster, some progress had already been made in developing Xen crystal technology. Adrian Shephard encountered a teleport in the underwater labs that fired beams from a yellow crystal; this was probably a Xen crystal or some synthesized imitation. The energy turrets that Adrian used to defeat the Gene Worm at the end of the Black Mesa incident had similar small yellow crystals attached to them, suggesting that the weapons fired exotic particle beams, similar to a crude Pulse Rifle. It is likely that the Displacer weapon also contained a piece of Xen crystal, since it was a fully functional teleport and yet a very small and portable device. The Gamma Laboratories had a teleportation machine known as a Displacement Beacon that used three Xen crystals in its power matrix. After the Combine invasion Dr. Eli Vance had a Xen crystal attached to the teleport in his laboratory at Black Mesa East, suggesting that Dr. Vance and Dr. Kleiner had somehow used the properties of Xen crystals in their new teleportation processes. This may explain why their machines could be so small compared to Combine teleports, and yet more versatile. Near the end of Episode Two, Dr. Kleiner remarked that he must remain in the control center to activate the xenium resonator; seeing that the crystals were originating from Xen, it is possible that Xenium is their scientific name (though fanon sometimes refer to them as Xenite).
Black Mesa scientists were making use of Xen crystals long before the resonance cascade disaster – the first teleportation experiments were only able to go to the Xen border world and not other locations on Earth, and as a temporary solution to this problem scientists created a relay device in the border world. The focus emitters were attached to an especially large Xen crystal, and it was this crystal that acted as the relay, receiving the teleport field and transmitting it back into our universe. During Black Mesa East, Dr. Mossman states that "Doctor Kleiner compressed the Xen Relay far beyond anything he'd imagined at Black Mesa. We've figured out how to use Xen as an unexpressed axis, essentially a 'dimensional slingshot', so we can move around the borderworld without actually having to pass through it". This statement seems to imply that The Resistance had somehow developed teleportation to the point where the Xen Relay was nothing but a mathematical artifice, rendering the device on Xen pointless. At the end of Entanglement, Dr. Mossman said that she "reprogrammed the modulator to emulate a Xen relay"; she is probably referring to this procedure of 'emulating' the relay instead of actually using a physical link like the device on Xen. It is probable that the Combine desired this sort of 'local teleport' technology, as Mossman states that the were unable to perform teleportation within the same universe and were therefore reliant on conventional transportation. This is probably what the Nova Prospekt portal was to be used for.