The Alkali Lake Incursion was a mission from the original timeline that saw the X-Men teaming up with Magneto and Mystique to break into Alkali Lake to save the captured students and stop William Stryker from using Dark Cerebro to kill all mutants.
William Stryker has kidnapped Professor X, Cyclops and a group of young mutants holding them in his facility at Alkali Lake. He plans on using his son Jason Stryker to manipulate the Professor into using Dark Cerebro to kill every mutant on the planet. The X-Men must team up with Magneto and Mystique to stop Stryker and save all mutants.
Magneto informs the X-Men that Stryker broke into the Mansion not to kidnap the children but so he can copy cerebro and build his own. He wants to use the kidnaped Charles and the fake Cerebro to kill every mutant on the planet.
Together Storm, Jean, Wolverine, Nightcrawler, Magneto and Mystique break into Stryker’s base at Alkali Lake. Mystique uses her disguising abilities to get into the control room and find the location of the captured mutants also Professor X. in Dark Cerebro. Storm and Nightcrawler save the captured students, while Jean is forced to fight a mind controlled Cyclops, and their fight causes major damage to the dam that Alkali Lake is built in. Back in the X-Jet, John, Rogue and Pyro are waiting for the X-Men to return, Pyro however is fed up with being treated like a child and leaves.
Wolverine tracks down Stryker but is forced to fight Lady Deathstrike, in the same room that gave them both their adamantium. Wolverine kills her by pumping her body full of adamantium, however, he shows remorse since she was just a slave controlled by Stryker. Jean (now injured) and Cyclops manage to make their way, through the labyrinth of tunnels in the facility.
Jason is mentally manipulating Charles with illusions, posing as a young girl back in the mansion, asking Charles for help locating the other mutants, he activates Dark Cerebro causing all mutants in the world to experience massive psychic pain. Magneto (who is shielded from cerebro due to his helmet) finds Charles but instead of saving him he reconstructs Cerebro so that it will kill all the humans instead. Magneto and Mystique leave but are joined by Pyro who decide to join the Brotherhood.
Stryker leaves the complex, but Wolverine finds him and angrily punches him into submission and impales him with his claws. Wolverine demands answers, such as why he bonded him with the Adamantium and why erased his memories. Stryker only tells him that he'd volunteered for the procedure and that the two of them worked together. He says Wolverine is a failed experiment, that he was an animal before and an animal now. Wolverine chains him to the helicopter and goes back for the others.
Storm and Nightcrawler find Professor X. and save him before he can proceed with killing the humans. The X-Men now with the captured students, Cyclops and Professor X. prepare to leave as the dam is exploding but find the helicopter missing. Luckily, Rogue arrives piloting the X-Jet with Bobby. Cyclops and Storm take over control of the Jet but it begins to malfunction just as the dam breaks. Jean leaves the jet and uses her telekinesis to stop the water from destroying the jet and killing everybody. The X-Men reluctantly manage to escape but Jean is seemingly killed as water engulfs her and destroys the facility also killing William Stryker, who Magneto had trapped using metal chains.
The X-Men visit the President informing him that the attack on his life and the massive psychic attack, were the plans of William Stryker and not mutants. He agrees that mutants and humans should find a way to coexist in peace. Back at the X-Mansion, Bobby and Rogue become official members of the X-Men. Cyclops becomes emotionally devastated by Jean's death, but back at the flooded Akali Lake, a fiery Phoenix-like shape rises from the water.