This Story takes place in year 100 of the X-men. Apocalypse is meeting with Wolverine, Cardinal and Rasputin where we learn about his new Horsemen of the Apocalypse. It's also worth mentioning that the tree person is the mutant Cypher who's body melded with the infrastructure of Krakoa. The one with the flaming Skull is the mutant Xorn and the Magneto figure is a second generation Chimera created by Mr Sinister who's name is North and is a mix between Polaris and Emma Frost.
Jumping over to Omega Sentinel and Nimrod, they're trying to figure out apocalypse's endgame. This is the point where we learn that the machines weren't put in charge by the humans. The humans were always thought to have modified themselves out of their own free will but we were all wrong.
Omega Sentinel has gone to look for the mutants who are attacking a church. The church worships the machines and believes that the machines are their salvation. Simply just a show that describes how fear clouds judgement. This church is branding children with machine parts.
Luckily, that's when the mutants show up. Cardinal, Xorn, Rasputin and North. Their mission is to try to save the mutants. That doesn't mean that they can't save humans from themselves.
That's when Omega Sentinel arrives with a squadron of Sentinels and all hell breaks loose. During this battle we get some helpful exposition which explains that Cardinal is so violent because of Apocalypse when he should be a pacifist. North also gets obliterated. Rasputin and Xorn are the only ones left. Rasputin luckily has an ace in the hole though. Xorn's mask contains his true power. He can release a singularity. So she and Xorn do at the cost of their own lives.
This assault was all a distraction though. Apocalypse, Cypher and Wolverine have made it to the data storage for the information taken from every mutant's mind over their years of captivity. They've come to steal all of it. But Nimrod figured this out. This was the mutant's endgame. Wolverine and Cypher escape but Apocalypse stays to distract Nimrod. To battle him to the death.
The person that Wolverine gives the information to is Moira Mctaggert who's been sleeping for at least one hundred years. But Wolverine's job was to give her the information and kill her. Moira understands this and she accepts it.