TL;DR at the bottom for those who don't want to read everything.
Xavier and Magneto vs Orchic, Omega Sentinel and Nimrod. The mutants ready to die for their cause. Nimrod and Omega Sentinel say that the humans don't matter, since it's a battle of the titans. So they start killing them. Omega then explains to Xavier that she hates humans as much as she hates mutants. The four battle, with the grandpas getting their asses kicked.
Back in Moira's No-Space, Moira tells Mystique and Destiny that they can't kill her, or her powers will reset everything. Mystique is all "lol" and shoots her anyway. And then... and then... and then...
The Death of Moira X.
Flashback to the past. Emma, Destiny and Mystique are talking. Emma explains that while Xavier looks into someone's mind, he sees their strengths. She sees their weaknesses, and when she read Moira's mind, she noticed Moira was trying to hide things from her, so Emma took a peak. She tells them about Moira's tracker in her arm. She gives them Forge's gun that turns mutants human. Mystique goes on to disguise herself as Sage to hack Krakoa's database and find Moira, then becomes an Orchis agent to infiltrate Terra Verde, chop off Moira's arm and take Moira away.
Cut to now. Mystique says that she's given Moira what she wanted: she's now human. Destiny confirms Moira's suspicions, they made her human so they can kill her. Destiny also says that she can't see shit because it's like a nexus point; there are so many possibilities that stem form their actions right now. But they want to lock in their good future.
Moira asks if it matters at all that she doesn't believe in it. Mystique says that no one cares about a traitor's opinion. Moira says that they've always lost, she's experienced this for thousands of years. Mystique and Destiny are mere children to her, talking about hopes and wishes. And then the truth comes out: Moira wants to save mutants from their fate. She wants to cure them. Moira has a cure in mind, one that cures anymore before they manifest. Kids grow up, not knowing what they lost.
Meanwhile, the golden guys are fighting the robots. Magneto turns Omega's body against her. Nimrod has Xavier, and Xavier tells Magneto they can't die, or else they'll lose their memories of what has happened and they won't know that Moira isn't with them. So they negotiate, where Nimrod and Mags will stay and fight while their friends leave. Magneto agrees, but Nimrod is all "lol psyche" and kills Xavier anyway. Magneto kicks Nimmy's ass. Omega uses a power dampener to fuck him over.
With Mags on the ground, Omega talks about how machines are made as tools, then people try to destroy them when they turn into something more than that. She shoots Mags and kills him, but is sure they will inevitably meet again.
Suddenly, Hellion flies in and punches out Nimrod with his rocket fist. Since his hand is metal, not mutant, Nimrod can't do anything to stop it. Hellion expands a telekinetic barrier in the open wound he created in Nimrod's head, blowing him up. Nimrod can't heal because the space is occupied, and he dies.
Time skip to four months later. Hellion is now part of the Council. He's begun to restructure, and a new Quiet Council has been formed. It includes Laura, Wind Dancer, Tag, Dust, Wither, Mercury, Surge, Rockslide and Prodigy. Rockslide seems to have recovered from his Otherworld misadventure, since he makes a rude and boisterous remark about the old Council. Tag also mentions how much of a mess the old Council made, and how he (the new head of Hellfire Trading) has to clean it up.
We get an preview for Immortal X-Men, which is about the deposed Council. They call themselves the Quiet Council, and they represent the old regime. The New Council has been elected by the people of Krakoa, while the Quiet Council live on Arakko and want to reclaim their old position. Storm's pissed that she lost her crown, but Hellion thought that Dust was more deserving. Unbeknownst to them, Trance is spying on them with her astral projection.
The Krakoan at the end reads CHOOSE YOUR DESTINY.
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Okay, those last three paragraphs and Krakoan didn't happen. No Hellion fighting Nimrod, no new Council. Instead, we cut back to the bisexuals. Mystique is about to kill Moira when Doug shows up. Destiny pauses Mystique, saying that she's blind to Doug's actions because he "brings chaos and a breaking of time." Doug says that their plan has a small problem: if they made Moira human, killing her would break one of their laws. Doug is insistent they do the right thing. He says that "Those who are supposed to protect us always end up too busy protecting themselves to do the job. But that doesn't mean we can't be better." Mystique says she'll just kill him, but Doug says he won't die so easily. Doug reveals that he has Krakoa, Warlock and Bei backing him up.
Destiny can now see the future again, and they have three options: they can kill Moira, but Mystique will be exiled and Destiny will die six months after that. She won't be reborn after that. Option 2: they try to kill Doug and fail. Mystique dies and Destiny stays on the Council. Mystique maaaaaay be revived in about three years. Option three: they let Doug win and free Moira. All three of them remain on the Council and consolidate power. They pick option 3.
Warlock gives Moira a techno organic arm. Doug says that he doesn't care where Moira goes, since it'll probably be better than here. She's free to go wherever she wants, but the gate will seal itself to her afterwards. Moira asks if they'll wish her luck; Doug says no. Warlock does, but calls her a "self not friend."
A week later, Emma revives Mags and Charles. Emma reveals that in the time they were gone, she told the Council everything. They decided that keeping the secrets wasn't wrong, but they should have shared it with the Council instead. She gives him back Cerebro and welcomes him back. The end.
No Krakoan at the end. We just get a page that mentions Immortal X-Men.
TL;DR: Mystique uses Forge's gun to make Moira human again. Doug saves Moira and lets her escape. Warlock gave her a replacement TO arm. Mags and Xavier die fighting the robots, but Emma revives them a week later. The Council knows everything about Moira and they decide not to keep secrets from each other.