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Not much is known of the Dark Presence's origins or how it came to be trapped within Cauldron Lake. It boasts itself to be much older than protagonist and writer Alan Wake thought before, but the exact date as to its beginnings are never made clear, be it in-story or through supplementary material.
The Presence has the ability of warping reality according to the creative mind it latches onto, mostly writers like Alan Wake himself or Thomas Zane, but it can also bring to fruition song lyrics and music, as it was the case with the Anderson Brothers. It works as an editor to these works, in its own twisted way, trying to take advantage of plot holes and Deus ex Machina to make itself stronger and, if successful, escape its confinement.
Like many other Eldritchian horrors, it doesn't have a proper form of its own, mostly being depicted as a black fog or smoke, moving about in the air as if underwater, and choosing to take other forms to manifest itself, such as animals, objects, and the people it possesses, either to be its avatars or Taken minions.
The Poet and the Muse
While the Dark Presence has been rumored to have used several writers through history to further its own machinations, writer Thomas Zane was the first to awaken the Dark Presence in a far more intimate, dangerous level, during his stay at Bird Leg Cabin in the 1970's. Throughout the course of his stay, Zane realized the Lake's powers and used them to further his poetry and stories, but it quickly started to grow out of hand. Thomas' lover, Barbara Jagger, while swimming one day, drowned under mysterious circumstances (it's hinted often that the Dark Presence, by itself, pulled her deeper under the water). Desperate, Zane attempted to write her back into life using the lake's power (an act suggested by his then-assistant writer, Emil Hartman), but what did come back was the darkness, using Jagger's visage as means of communication with the outside world, and to manipulate him into releasing it. Realizing his mistake, the writer attempted to cut out her heart, only to discover it, even in human form, had none. Without options, Zane wrote himself and the Cabin out of reality by sinking it and Diver's Isle in a volcanic eruption (Cauldron Lake has its name from being over a caldera), but not before leaving one final page written to bring in Alan Wake into the city of Bright Falls, in a last-ditch plan to subdue the Dark Presence.
In the meantime between the island sinking and Alan's arrival in Brightfalls, the Dark Presence was also responsible for the disappearance of FBI Agent Robert Nightingale's partner, and Hartman would go on to earn his doctorate and build Cauldron Lake Lodge, in an attempt to harness the lake's power for his own goals. The Anderson Brothers (Tor and Odin) would also be attacked by the Presence and survive it, but at the cost of their mental sanity, enough so to be interned at the Lodge. Once Alan did arrive in Bright Falls, the entity under the lake waters stirred yet again.
Events of Alan Wake
Upon Alan and his wife Alice's arrival, the Barbara Jagger avatar handed over the keys to Bird Leg cabin to the couple, tricking the two into heading towards Cauldron Lake. Once there, the Presence took Alice hostage underwater and controlled Alan's mind into writing the script of his next novel, "Departure", turning it into a horror story where the Dark Presence would come out of the lake and take the world under its shadows. Alan freed himself from the darkness' hold for enough time to let him write the story differently, keeping it a horror genre while creating new ways and fail-safes to ensure the Dark Presence would be cornered, including writing Zane into the story to take away the manuscript's pages and leave it unfinished for enough time to develop a counterattack. Alan then escaped and the story, as he rewrote it, was set into motion.
His journey was not easy, however. The Dark Presence attacked him, his allies and the city itself with its own
fabrications, such as the Taken, Poltergeist objects and giant dark tornadoes hurling debris. Hartman's plot to control the Presence through his patients' creativity ended with Wake throwing him into a room with the darkness taking over his lodge and presumably dying, and Nightingale's insistent chasing was stopped when the Presence began invading Bright Falls itself, taking the Agent out in a fell swoop through a door. Alan, his agent Barry and Sheriff Sarah Breaker, with the help of Zane's former admirer Cynthia Weaver, were able to locate the one thing able to cause the Dark Presence to retreat: a small switch nicknamed the "Clicker", from Wake's own childhood. Diving into the waters of Cauldron Lake and arriving at the Dark Place, Alan used the Clicker within the hole in Jagger's body and successfully defeated the Darkness, releasing his wife back to the real world while being trapped underneath Cauldron Lake by himself. Alone inside the Dark Place, Alan would eventually fight off the Presence's attempt of taking his mind and begin the process of his return.
Alan Wake's American Nightmare
During Alan's time imprisoned within the Dark Place, where the Dark Presence resided, he wrote a script he used to manifest into the real world yet again, this time fighting off the Presence's second avatar, an evil copy of himself known as Mr. Scratch seeking to steal Alan's life for itself. As before, the Dark Presence attempted to attack him through the doppelganger, who was far more sentient and intelligent than the Presence itself, utilizing many new forms of Taken and reinforcing the Poltergeists into truly deadly opponents. However, thanks to Alan's persistence, Scratch was destroyed and the writer found himself at least a few steps closer to finally returning to the real world fully, even if the battle against the Darkness wasn't done yet.