When Cyclops and his mutant revolutionaries destroyed the black hole at the Brookhaven National Laboratory’s Large Hadron Collider and saved the state of New York, they became heroes. Cyclops reunited the X-Men and became a political leader, championing pro-mutant rights and people excluded from power. Following that, he was elected President of a dangerously divided United States with the Hellfire Club trying to oust the X-Men from power, and the Eugenics Society working to restore anti-mutant sentiments.
After his inauguration, Scott is unable to sleep. A fervent protest carries on outside the White House. His wife, Emma, brushes it off as stress, oblivious to the bigger picture of civil unrest that weighs heavily on Scott’s mind. Emma telepathically coaxes Scott to sleep.
Suddenly, the Phoenix force appears and wipes Emma from existence.
Flashback to the inauguration after party, the X-Men, Avengers and other superheroes are partying. Emma has invited the Hellfire Club, which does not sit well with Scott. He excuses himself from the party. Shaw tells Emma since the Hellfire Club helped Scott win the election, he expected a “favour” in return.
As Scott watches the protest outside the White House, he reflects on his journey from “S.H.I.E.L.D.’s most wanted terrorist” to becoming President. He ran on the platform of “equality for all”, believing it would finally atone for the murder of his mentor, Charles Xavier, who championed peace between mutants and humans. But on this very night, Scott finds himself giving an executive order to deal with the protesters by using “any force necessary”. He does not see another other choice: the peace was just a fantasy.
When the protesters saw the flames of the Phoenix, they interpreted it as judgement from God. Some protesters ran, while others stormed the White House.
Logan quickly organises the X-Men into two teams: one to deal with the protesters, and another to check on Scott. The Cuckoos, Shadowcat and Beast awaken Scott but he is only distressed because Emma is gone. Because Emma has been wiped from existence, everyone has not recollection of her. Scott claims that they were married and grabs the wedding photo to show them. The wedding photo is one of Scott and Jean. Beast thinks Scott is delirious because Jean, his wife “has been dead for years”.
Scott suggests that Emma could have been kidnapped by the extremists who are protesting, and the X-Men given a “memory wipe”. Beast is not convinced with Scott’s theory because the only two telepaths capable of wiping their memories are dead. Shadowcat adds that it seemed pointless to only erase their memories of one person. But Scott has made up his mind to go outside to confront the protesters.
Scott appeals to the protesters to surrender Emma or face justice. In the crowd, one of the protesters pulls out a handgun and fires a shot at Scott. Shadowcat leaps in to stop the bullet but it phases through her and strikes Scott in the chest. Chaos ensues when a gunned down Scott loses control of his optic blasts, killing hundreds of protesters in the process.
While Triage works to save Scott’s life, Logan and the others work to save the surviving civilians. Meanwhile, viral footage of Scott’s massacre is making the social media rounds. Even when he is bleeding out, and all the peace they had fought for has fallen to the wayside, all he can focus on is finding Emma. He instructs the Cuckoos to search for an “omega-class telepath”. Shadowcat adds: “powerful enough to create a memory wipe” and “block Cerebro”.
Shadowcat brainstorms to use the “lockbox program” to track down the omega-class telepath. But she and Beast makes a startling discovery: mutants and humans are gradually being wiped from existence all over the world.
Suddenly, Scott finds himself in the “White Hot Room” of the Phoenix. The Phoenix had erased mutants and humans from the world because the world is not ready for a mutant President. The future only brings “war and disaster”. But the Phoenix gives Scott a chance to “change this future” by “undoing the past”.
Phoenix: “But you still have a chance, Scott. You can still change this future.”
Phoenix: “By undoing the past. Come. The past awaits, and so does the possibility of a better future. The power of the Phoenix combined with the life-force of the X-Men can transform time and space.”
Scott: “Will I remember this life?”
Scott: “Will I be happy?”
Phoenix: “You will have your heart’s desire.”
The new alternate timeline shows Scott and Jean happily celebrating their wedding anniversary, surrounded by their friends and team mates.
Scott: (Thoughts.) People say that in life, there are no second chances. But sometimes we get lucky.