While the primary Age of Apocalypse issues were set in the "present day" part of the timeline, they did think to provide us with a prequel to those stories in the X-men Chronicles series. This title replaced X-men Unlimited, which was basically just a series where Marvel was squeezing even more money out of us X-men fans by providing outside-of-the-main-storyline character pieces in double sized issues. In all fairness, a lot of these stories were really high quality in large part due to that longer length.
X-men Chronicles #1 is clearly meant to be the Age of Apocalypse version of Uncanny X-men #1, aka the very first appearance of the X-men. It's a fantastic idea to take a turn of events most X-men fans are very familiar with, and turn it on its head so that we can see how this universe differs from the one we know.
First off, we learn that in the wake of Charles Xavier's death, Magneto was greatly changed. Rather than trying to dominate the humans, he now chooses to hide himself and his mutant recruits away from the world. I like that he's not so changed as to dream of peaceful coexistence, as that would simply not be very believable for his character. But he is still training these students to prepare them for a coming war, and after learning that his son Quicksilver is naturally a member of his X-men, we also find out the name of their training area - the Killing Zone. I think changing the name from "The Danger Room" to "The Killing Zone" tells us so much about Magneto's methods versus Xavier's without having to over explain it.
These X-men uniforms are very reminiscent of the original X-men costumes, but with red instead of blue, fitting to match their leader. I think this team largely makes sense - we've got Quicksilver and Scarlet Witch because they are Magneto's children, Iceman and Jean Grey from the original team, and Storm, Colossus, and new recruit Weapon X (aka Wolverine) from the second wave of the team. All of these characters have strong power sets that would attract Magneto and make him want them on his side. Where the missing original members are will be explained in future AoA issues.
This Logan is still completely wild, and in the absence of Xavier, Magneto immediately tasks Jean with controlling Weapon X's berserker rages. She mentions that her telepathic powers are not very strong, so I'm not sure if this version of Jean had her telepathic powers dampened by Xavier before he was killed or not. Logan still flirts with her constantly, which is a little disturbing since this is a fairly young Jean here. That's one of the things I found frustrating while reading this. The exact amount of time before current events isn't entirely clear. Obviously, comics don't move in real time, so we can't consider this the 1960s with the current time being the 1990s, but I would have liked a little more explanation as to how many years before this occurred.
Regardless, we get one more new recruit, as Mystique shows up to drop off Rogue. It's once again a good parallel to Rogue joining the X-men in the main timeline, as she's coming here because Mystique cannot protect her from Apocalypse nor really deal with the fact that Rogue just absorbed approximately half of Polaris' powers. While I understand that it had to be someone other than Ms. Marvel that Rogue absorbs, using Polaris feels just a bit too convenient here. Essentially, Rogue and Magneto had a history in the regular timeline, so they're finding a way to shove them together here and also be allowed to touch each other. I do think it's cute that they have Iceman hit on Rogue to parallel the moment where Beast hits on Jean in Uncanny X-men #1.
That's my girl.
This group is made up of Gideon, Candra, Sabretooth, and two unidentifiable characters playing War and Death. Using those two makes me wonder where Famine and Pestilence are, but I guess we'll just assume they're causing havoc elsewhere. Gideon and Candra were both part of a very 90s group of villains called the Externals, and I think they are used primarily because the Externals are immortals and therefore would be fully fledged powerful adults at this point in the timeline. Sabretooth is here to fight Weapon X, of course. What is strange is that he gets upset when he finds out that they plan to actually launch the missiles. I guess he thought they were going to just bribe the government or something? Being upset about the world blowing up doesn't really strike me as in-character for Sabretooth, who I've always seen as a psychopath on par with the Joker, but with strength, healing factor, and claws besides. He is a wild animal like his name suggests. But now he has a conscience... because? He is still a dick though, as he eventually shrugs it off and decides he'd rather stay on Apocalypse's side as he's the most likely to win.
Weapon X puts a claw through his spine though, and Apocalypse deems him unworthy. Magneto stops the missiles from launching, and Apocalypse retreats, confident that he may have lost this battle but he will win the war. That certainly seems true, because as this was happening, a character who identifies himself as Nemesis has attacked the X-men's base on Wundergore.
He tears stuff up pretty good and manages to kill the Scarlet Witch, who Magneto had tasked with staying behind to protect their home. Oops. With her dying breath, she begs Rogue to befriend her father because "he needs love." I don't think Wanda meant to go literally love him up though, Rogue.
But we do get this really good picture of Magneto holding the Scarlet Witch, a perfect sign to show us that this reality is a cruel one, and we shouldn't hope for any hero to survive.
Overall, I'd call this a good issue that really helps explain the beginnings of this universe. The art is decent and while it does rely on some old comic book tropes ("Must... explain... what I'm doing.... in thought bubbles!") the writing is good. I get the feeling this was rushed to release though - I caught at least three typos and grammar mistakes, and Rogue uses "I" once instead of her trademark "Ah." Marvel editing was usually pretty good at this point, so a lack of time is the only excuse I can think of for that.