First off: Just found this story awhile ago and gotta say it's looking good so far, a bit short chapter wise but still good nonetheless.

The Institute and Enclave working together is a bit unexpected (In a good way), definitely like that twist.

Also especially like how militarized the Minuitemen is in this story.

One question that's on my mind: Since Mark and John were US Army Rangers wouldn't they have known Lieutenant Taggerdy and to an extent Roger Maxson?
Maybe they have (unknown to them) connections to the Brotherhood of Steel: In the Codex/referenced by Roger Maxson himself via written entries about his past experience in the Army. I mean given the fact he was close friends with a Army Ranger Lt. means he could've likely been their CO before being transferred to West-Tek/Mariposa Military Base.

Since this takes place during the early stages of the Brotherhood/Enclave War wouldn't the Minuitemen eventually down the line send a small Expeditionary Force to D.C. to aid the Brotherhood of Steel?
(Since at this point the Brotherhood and Minuitemen share the exact same goals.
Well technically since the Brotherhood was originally founded by Roger Maxson and his men to help rebuild civilization)

Keep it up! Will definitely like to see how this AU goes. So far I'm impressed.

Ok I got a couple to unpack here... I won't harp on the minor grammar/typo errors since those are kinda negligible:

The first chapter where you explain backstory... From what I've read so far, most of it was mentioned in the subsequent chapters. Maybe instead of making a whole chapter for the backstory like that, maybe you could have characters mention said backstories or write about the experiences directly.

Also, I assume that you decided to make the entire story of Fallout 4 happen at the same time as Fallout 3 since the Quincy Massacre happened not too long ago in 2287. But what is the state of the minutemen? Are they the same as in Fallout 4, basically in shambles? Because from what I understood, it seems that they're still at least a small mercenary outfit with a command structure and all so I found it kinda weird that John and Mark are able to take command of minutemen soldiers even though they just met said soldiers. That and the informal way they interact with Hollis (both on and off combat) since all 3 of them are military vets so yeah.

Overall, your story is quite good and has its own unique take. I like it. And if you want to improve on your storywriting ability, I suggest checking the Youtuber, hello future me specifically his "on writing" series. Good luck with your endeavors dude! Cheers! :)