Alkali Lake is the name of a military complex located in Alberta, Canada. It is also the name for a secret military base hidden underneath the surface of the military complex. The complex is located on the inside of a dam, surrounded by a freshwater lake with the same name, as well as the Canadian Rockies. The base is known to be the site of the Weapon X program, as well as multiple experimentations on mutants. It is unrelated to the Alkali Lake community located in British Columbia, Canada.
Major William Stryker operated Alkali Lake as the facility where the Weapon X project was created. Following Logan's escape, Stryker declared the facility unsafe and moved his base of operations to the Three Mile Island facility.
After Logan joins the X-Men after wandering around Canada aimlessly, Charles Xavier tells Logan about the existence of a military compound at Alkali Lake in the Canadian Rockies, which might help him restore his memories. Logan steals Cyclops' motorbike to travel to Alkali Lake.
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Upon arriving at Alkali Lake, Logan finds the facility abandoned, and returned with no clues. After Charles Xavier went with Scott to visit Magneto at his plastic prison, Yuriko Oyama intercepted the pair and captured them both. Charles and Scott were taken to Stryker's facility at Alkali Lake, where Scott was brainwashed via Jason Stryker's spinal fluid and Xavier was controlled by Jason himself to activate Stryker's Cerebro.
The X-Men team up with Magneto's Brotherhood, whereupon Magneto explains that Mystique uncovered plans for a second Cerebro in Stryker's base, but the location of this base is thus far unknown. Jean Grey uses her telepathy to examine Nightcrawler's mind, and discovers Stryker's base is at Alkali Lake.
In the X-Jet, they discuss how to break into Alkali Lake and prevent Charles from wiping out all of the mutants via Cerebro. Mystique poses as Logan to enter Alkali Lake, given Stryker would want to see his creation again. She breaks free and enters the control room, where she unlocks the main spillway mechanism, allowing for the X-Men and Magneto to enter the base.
The group splits up, with Jean heading Magneto and Mystique to find Cerebro, and Storm and Nightcrawler heading to find the children Stryker captured from the X-Mansion. Logan goes off on his own, where he finds the tank that he received his adamantium skeleton in. Stryker approaches Logan with Yuriko, and states that he no longer sees Logan as "one of a kind". Logan fights Yuriko, eventually killing her by filling her body with adamantium.
Jean holds off a brainwashed Scott sent to prevent them from reaching Cerebro, allowing Magneto and Mystique to continue on their way. Kurt and Storm rescue the mutant children. In their fight, one of Cyclops' optic blasts disrupts the integrity of the pressure of the dam, indicating that it is about to burst its banks. Magneto stops Xavier from killing every mutant on the planet in the nick of time, but reverses the procedure to target humans instead.
Stryker tries to flee in a chopper waiting on standby, but Magneto's change of plans causes him to become affected by Charles using Cerebro to kill the humans. Logan stops him from escaping and chains him to the chopper, stating "if we die, then you die." Magneto and Mystique approach an immobilised Stryker, taking the chopper and chaining Stryker to a separate wall.
The X-Men try to take off in the X-Jet, but the landing gear was damaged by Rogue's flying. Jean exits the X-Jet to allow for the X-Men to take off, but she "dies" in the process. Stryker is drowned as well as Alkali Lake is destroyed by the dam bursting its banks.
Scott, still traumatized over the death of Jean, begins hearing psychic whispers from her. Tormented, he travels back to Alkali Lake, where he is astonished to see that Jean is still alive. They kiss, but her psychic powers vaporise him. Logan and Storm are sent to Alkali Lake to investigate, where Logan finds Scott's red glasses and Jean. They take her back to the X-Mansion, where Charles theorises that her powers protected her in a cocoon of telekinetic energy as the dam at Alkali Lake burst its banks. Although this now seems unlikely in the revised timeline, Alkali Lake may have been nothing more than abandoned ruins.
The mutants and Moira are held in a cell to be questioned by Stryker about Xavier's whereabouts.
Meanwhile, Scott, Jean and Kurt are looking around the base for them, until they come across a container in a lab with something alive and angry in it. Jean uses her telekinetic abilites and opens the container. As the guards arrive, out from the container emerges Logan AKA Weapon X, who attacks the guards and goes on a violent rampage through the facility. Stryker is told about Weapen X being loose and he escape. Before Weapon X flees the facility, he is approached by Jean and he calms down. Jean removes his helmet and taps into his mind and restores his memory and he runs away.
Scott, Jean and Kurt finally rescue the others and make their way to a hanger where they discover a jet and a supply of battle suits. They suit up and take the jet to Egypt.