The San Diego police have been brought in to investigate the scene of destruction at the Tomahawk Motor Lodge.
Cyclops is livid that they had been so easily defeated, in part due to Michael turning his back on their offer to help and give the Alliance the upper hand in defeating X-Factor. Analysis of the situation turns in to a heated argument between team members. Marvel Girl lashes out at Cyclops, feeling that he blames her for not being the Phoenix anymore.
Cyclops: “They shouldn’t have been able to sneak up on us...we should have had warning!”
Marvel Girl: “You blame me for that, don’t you? Because I’m only me now...And not Phoenix! I’ll just bet nobody ever got the drop on Phoenix, is that it, Scott? Don’t you understand? That energy monster buried me in a cocoon -- stole my life with you and the X-Men! And now that I’m awake again everything has changed! Professor Xavier is gone...His X-Men are being led by our most vicious enemy...And I’m not a telepath anymore! I’ve tried to tell myself that I have other powers -- that it doesn’t matter -- But it does! I could read people’s feelings...Their thoughts…and now it’s like I’m in a jar with the lid screwed on tight! You’ve changed! You act like you hate me! You’re keeping things from me...But I don’t know what...And I don’t know why!
Angel tries to intervene but only adds fuel to the fire, culminating in a physical fight between him and Cyclops. And in the process revealing their mutant identities to the police, crowd and media waiting outside.
Realising that things are getting out of hand, they agree to settle differences later and hatch an escape plan before people start putting two together and find out that X-Factor are mutants. On top of that, Michael now knows who X-Factor really are and nothing is stopping him from blowing their cover.
Except that Michael has not been telling the Alliance the truth despite the torture at their hands. Michael’s story is that the mutants were battling X-Factor and drove them off before the Alliance showed up; that it was pure coincidence. The Alliance however isn’t buying the story and refuses to give Michael the heroin (which blocks his powers that the Alliance feeds off on in the first place). Stinger then got the bright idea to “beat on” Susan instead to make Michael talk. Michael goes ballistic and lashes out with full power, causing everyone’s power to go into overdrive, rendering most of the Alliance stunned and useless.
That ruckus causes a good-sized explosion that draws X-Factor’s attention. Cyclops is not so keen on helping Michael out, but Beast is insistent that they should do something to save Michael from ruining himself, as their ultimate goal is to help their own kind. Angel flies off to get a closer look at the location of the explosion.
At the house, Frenzy is ready to kill Michael when Apocalypse intervenes. He has ordered that Michael not be “damaged” as his power is to prove useful to Apocalypse. Apocalypse demands that Michael be returned to the “Monitor Machine” so he can run more tests. Frenzy disobeys Apocalypse, wanting to continually feed off Michael. Apocalypse disciplines her harshly. He is pleased however, to note the fighting spirit and willingness to turn on each other within the Alliance. Apocalypse’s ultimate goal is to weed the strongest mutants from the weak through mutants fighting each other, thus acquiring an army of the fittest mutants to rule.
That evening, X-Factor approaches the house and begins to infiltrate. Beast is instructed to scale the cliff face and “check the windows”, while Angel and Marvel Girl are to “reconnoiter through the hole in the roof”. Cyclops watches them with jealousy. Him pushing her away gives Angel the opportunity to pursue her affections. Iceman is the one left for Cyclops to vent his frustrations to.
Iceman: “Scott, keeping your marriage a secret from Jean...It’s tearing her apart! And you...Have you called Maddie?”
Cyclops: “There’s no answer, Bobby! I...I think she’s left me! Part of me wants to find her...Explain about Jean’s resurrection -- Why I had to go to her...Make her forgive me...Let me come home! But Jean’s back in my life now, high on X-Factor’s promise, eager to rescue a love-sick junkie loser...Flying in Warren’s arms, talking to him...Laughing...And part of me wants to punch their hearts out! I think I must be going mad!”
Angel and Marvel Girl make it through the hole in the roof but are discovered by the Alliance. Beast breaks in through the window, into the room where Michael and Susan are held. Beast is working on trying to free Michael, despite his urging to remove Susan to safety first and leave him. Apocalypse finds Beast and prevents him from freeing Michael.
Cyclops and Iceman are headed for the roof to help Angel and Marvel Girl. They are battling the Alliance when ‒Apocalypse’s platform rises” to the roof. Laying Susan’s life on the line, Apocalypse commands Michael to “increase the power of the Alliance”. X-Factor finds themselves no match for the more powerful Alliance.
In the heat of battle, Susan is killed. Michael is driven over the edge. His powers urge full blast again, stunning the Alliance. Apocalypse fears that Michael is going to kill himself and goes to “re-set the monitor”. Cyclops destroys the machine before Apocalypse can get to it. Instead of being furious, Apocalypse thanks X-Factor for showing what they are capable of, and that they are strong enough to serve Apocalypse’s cause in “winnowing out the weak”. Apocalypse leaves. The Alliance does too, but walks right into an army of police waiting below.
X-Factor watches as Michael slowly fades away, and realise that while they’re not their mentor (Professor X) and will “probably...never be as good” but “it’s how [they] handle [the situation] that’s the measure of [their] worth”.
Cyclops is also obsessing over the fact that he thinks he’s witnessed Marvel Girl displaying the Phoenix’s signature “bird shaped” flame, and that Phoenix might have returned.
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