So when I got my squire from the Brotherhood of Steel, I went to Gwinett Brewery and attacked him just because I felt like it. He started running away, but after about 30 seconds he just stopped and acted normally. Right after I left the brewery I went back to the Prydwen, and everybody started attacking me and my squire became an enemy and started running away. I tried to load a save before I attacked him, but it only shows my 4 most recent saves and a save when I first started the game. How do I get them to stop hating me?

UPDATE:

So I tried killing any important brotherhood NPC and it says I am no longer allied to them and fails my quests with them. That means that even though they are constantly trying to kill me, I'm still allied with them for some reason.

Ummmm, this isn't going to sound helpful right now, but it's golden for next time. Make more saves? When you say, "but it only shows", that makes it sound like you DID save more but they aren't showing up. Is that the case? If so, there may be something you can do.

But back to the main question...

I just did a quick search but I don't see any reputation fix hits. If they exist, they may still require having knowledge of things we don't have access to yet. Never underestimate modders, though, and keep your chin up and searching.

In new vegas and other games, a faction would have a corresponding address that stored the reputation, but in that case we were also dealing with Fame. There was a command to set the reputation level. I have no idea of the addresses in Fallout 4.

But I wouldn't get too discouraged... and I have a hunch I'm gonna try out. No promises, but I'll be back to post in a half hour or so and we'll see what I find.

FOLLOWUP:

I fired up the game and sat at the console for the last 40 minutes. I fired upon a Brotherhood Knight in a few different ways, focusing on difference of duration. Here's what I found... or didn't when that is the more appropriate term.

The commands "setally" and "setenemy" do exist and run. If you do not enter a proper faction, it responds with an error. There is also a variable called "HostileGlobalBrotherhoodOfSteel". It was set at 100.00 by default for me, but changing had no base effect. Also, it does nothing if you have attacked them and then try to change it.

My testing shows there's a pretty slim chance they'll show you mercy [using the patented "put gun away and pray to spaghettay" method] if you shot one of them more than a few times.

Using the console command "help" [syntax: help brotherhood 0, and help brotherhood 0 fact for factions specifically] I was unable to find a variable that affected their hostility toward me in a firefight.

I'm certain there IS a variable storing whether to shoot on sight. lol But I couldn't find it. Maybe this will point you, or someone else, in the right direction.

Here's a link to more in-depth commands with their syntax. I can't vouch for them all, but the ones I've used do work.

http://fallout.wikia.com/wiki/Fallout_4_console_commands

Yeah I save a lot, and I even saved before I started attacking the scribe but they aren't showing up, only 4 recent saves which are after I attacked him. I checked my Documents/My Games/Fallout4/Saves and I see a lot more saves than those 4 but I don't know how to use them since it doesn't show them in-game.

GO to load and hit the "t" character select button. See what that does.

Yeah, that's a really good suggestion.

I would also ask, just for clarification, if you see what looks like a down arrow indicator below the saves it shows. Sometimes people are so used to just using continue that when they actually have to load a specific save they don't notice you have to scroll down. Please don't think I'm saying you're stupid. lol I've done similar stuff before and it's good to rule out simple things first.

I did press T, I have 3 characters and on the one that's being attacked by the Brotherhood of Steel, there's seriously no other saves other than the 4 most recent ones and my first save in vault 111. I save all the time and I guess it overwrites old saves, even though I still see some of them in my Documents/My Games/Fallout4/Saves folder

How do you save?