The Crystals are mainly found on the bark of trees. They lay dormant until they activate themselves, which makes them glow. It is unknown whether they activate when they feel the presence of a human, or if they periodically do this. They give off an unusual energy signature. The crystal can somehow make people come up and touch it, which is how they "rope in" its victims. When they do, the individual will receive an uncomfortable electric shock, knocking them backwards, and the crystal itself will shut down, because the energy is now inside the person. The crystal can also somehow control's the individual's dreams, giving them terrible nightmares, in the form of whoever touched it. Each night, the nightmares can become more and more severe until it has the capability of killing them in their sleep, most likely scaring its victims to death. The crystals likely take the dream's form of the individual's worst fear (falling thousands of feet, being eaten by a Whale). They can be transferred from person to person by touch, as it needs conductive material as transport, including Atlantis' power conduits. (SGA: "Doppelganger")
The crystals were encountered by the Atlantis expedition in 2007, in their fourth year of operation on M3X-387. Dr. Meredith Rodney McKay thought the activated crystals can be used as a self-sustaining power source. Lt. Colonel John Sheppard felt compelled to touch it, which caused an energy surge. They see the crystal was "killed off" and went back to Atlantis, not knowing the crystal energy signature is in Sheppard and that the crystal had also morphed into a doppelganger or copy of Sheppard, displaying all the character traits of Sheppard's dark side. He touched Teyla Emmagan, which passed the energy to her. That night she received a nightmare she never experienced before, which actually made her afraid of sleeping again.
However, she passed on the energy to Dr. Jennifer Keller, giving her a very unpleasant nightmare. Ronon Dex thought that it was just a few isolated dreams, until he had one himself. They discovered it was the crystal, which took Sheppard as a negative presence in the nightmares. After the crystal was able to kill one of its victims, Dr. Kate Heightmeyer, they went back to M3X-387 to retrieve another crystal to learn from it, eventually finding a way to track the crystal with Atlantis's sensors. After its determined to be inside of Doctor Rodney McKay, he is isolated in a rubberized isolation room where a plan is come up with to use the Volsinii virtual reality technology to connect Sheppard into McKay's dreams to attempt to convince the entity to return to its crystal which is also hooked up to McKay. The entity eventually causes McKay to be swallowed by a whale, but is forced from McKay before it can succeed in killing him when Keller uses a defibrillator to restart McKay's heart. The entity flees into Sheppard himself where it battles Sheppard in an empty Gate Room with an active Stargate in the background. Displaying superhuman strength and agility, the entity easily beats Sheppard until McKay returns to the dream world using the virtual reality technology. McKay has realized that the entity is vulnerable to electric shock and as the entity confronts him, Keller shocks Sheppard with the defibrillator. The electric shock severely weakens the entity, forcing it to its knees. Now having the upper hand, Sheppard throws the entity through the active Stargate and out of his mind. With nowhere else to go, the entity retreats to its crystal which has been hooked up to Sheppard. The team then returns the crystals to their planet where the entire jungle of crystals lights up in response to their return. (SGA: "Doppelganger")
The entity within the crystal displayed powerful mental abilities:
- Telepathy: The entity was able to compel Lt. Colonel John Sheppard to touch its crystal, allowing it to transfer inside of him. A second entity nearly managed to do the same thing to Doctor Jennifer Keller even from inside a non-conductive container.
- Dream Control: Once inside a victim, the entity had a great deal of control over their dreams, turning them into horrifying nightmares from which the entity could grow stronger by feeding on the fear generated. As the entity's strength grew, it was able to kill its victims in real life by making them suffer a fatal incident in their dreams. However, this required the entity to remain within the victim as seen when McKay recovered after being swallowed by a whale when the entity was forced from him.
- Superhuman Strength: In the nightmares the entity generated, it displayed an incredible degree of superhuman strength, enough to effortlessly punch through walls.
- Superhuman Agility: In its fight with Sheppard in Sheppard's nightmare, the entity displayed a degree of superhuman agility with its jumps.
All the nightmares caused by the crystal takes form of Sheppard as the primary negative presence. They include;
- Teyla Emmagan; Sheppard, in his mutated form from "Conversion", fed on her.
- Dr. Jennifer Keller; Teyla was killed by an Iratus bug crawling out of her stomach, and Sheppard acted as if it was the "coolest thing he ever saw".
- Ronon Dex; Ran away from Wraith weapons fire, only to be knocked out by Sheppard, who later buries him alive.
- Major Evan Lorne; Thought Sheppard was a Replicator. It was apparently so traumatic, he sleepwalked and held Sheppard at gun point, threatening to shoot him until he was stunned by Ronon.
- Dr. Kate Heightmeyer; Couldn't get off the edge of a balcony, and was about to fall. Sheppard stopped Teyla from rescuing her. The severe event of experiencing it caused Heightmeyer to eventually die in real life, making her the first and only known fatality.
- Dr. Rodney McKay; Rowed through a storm towards Atlantis chased by a whale while Sheppard goaded him to give up. Once joined by the real Sheppard through virtual reality technology, a clown joins them in the boat due to Sheppard's fear of clowns. Ultimately eaten by the whale, but saved when Doctor Jennifer Keller shocks him with a defibrillator to which the entity is vulnerable, forcing it to flee into Sheppard.
- Lt. Colonel John Sheppard; Awoke to find McKay had been killed by the entity and is blamed by his friends. Confronts the entity in an empty Gate Room with an active Stargate in the background. In the nightmare, the entity displayed a degree of superhuman strength and agility, easily beating up Sheppard, punching through walls and performing inhuman jumps. Using the virtual reality technology, McKay would enter the nightmare and confront the entity who was then weakened by shocks from a defibrillator administered by Doctor Jennifer Keller. In its weakened state, the entity was no match for Sheppard who threw it through the open Stargate. The entity then retreated to its crystal which was hooked up to Sheppard.
- During the scenes featuring both the real Sheppard and the entity, it is possible to differentiate them as the real Sheppard is wearing a sweater while the entity wears Sheppard's uniform jacket.