Alright, it took a lot of digging both online and in the GECK itself, and a lot of trial and error, but I think I found a combination of commands that work.
Dismiss Boone if you have him as a companion, then before going to the fort, run (the order matters):
setreputation 000f43dd 0 1
resetquest 00167f0f
resetquest 00129d14
setstage 00129d14 1
resetquest 001227a1
setenemy 000ee68a 0001b2a4 1 1
Close the console and wait up to five seconds. You should see the message saying the "Render Unto Caesar" quest was added. Now you should be able to travel to the fort as if nothing happened. Here's a quick breakdown of what the commands do:
Remove "Beware The Wrath Of Caesar" quest:
setreputation 000f43dd 0 1
resetquest 00167f0f
Fix "Render Unto Caesar" quest:
resetquest 00129d14
setstage 00129d14 1
Fix "Caesar's Dialog" quest:
resetquest 001227a1
Un-hostile the Legion:
setenemy 000ee68a 0001b2a4 1 1
Since I've been figuring this out for about two days now, had to learn the hard way that a lot of information online is wrong or not relevant, and went back and forth on thinking this might just be impossible, I want to take a second to document how the solution works for anyone having similar trouble.
There are three quests that are relevant to this problem:
- Render Unto Caesar is the quest you get after exiting the Tops, from the Legion guy that tells you your sins are forgiven and Caesar wants to talk to you.
- Beware The Wrath Of Caesar! is basically "the quest to fail Render Unto Caesar". It first shows up if you piss off the Legion after having started Render. You can piss them off either by advancing certain other quests, or by losing reputation with them (say by killing the hitsquads which for some stupid reason keep showing up even when they're not supposed to). Piss them off too much, and both this quest and Render are marked as failed.
- Caesar's Dialog. This is a hidden quest (doesn't show up in your log) used by the game to track what Caesar should say to you when you talk to him. If you don't clean up the quest variables properly, it's possible to get all the way to the Fort with the Legion non-hostile, but be unable to talk to Caesar.
In theory, I think all you would need to do to able to talk to Caesar is un-hostile the Legion and reset the Caesar's Dialog quest, executing only the last two commands, above. I just thought it was best to do things as cleanly as possible.
Resetting Beware
You might have gotten into this situation without ever starting the Beware quest, in which case you might not need to do this. Check your quest log to see if it's there (it's probably greyed out, i.e. completed).
Running resetquest basically makes it like you never even got the quest in the first place, which is what we want - just as if we never did anything to annoy the Legion after getting the Mark of Caesar. If you try to just run resetquest 00167f0f, what you should find is that if you wait five seconds (quest-related code runs once every five seconds, which is why it can take a while for quest console commands to take effect), the quest will be added straight back. This is because the logic for this quest is: the quest begins if you have low reputation and you possess the Mark of Caesar that you get from the Legion guy in New Vegas who invites you to talk to Caesar. So if your rep is still slow, the quest will start up again once the game does that check.
So, you have to reset your reputation with the Legion with setreputation 000f43dd 0 1 before resetting the quest. 000f43dd is the code for the Legion, 0 means you're setting reputation (as opposed to fame), and 1 is neutral (higher rep means they hate you more).
Resetting Render
This is straight forward. resetquest 00129d14 removes the quest from your log as if you never got it, and setstage 00129d14 1 starts it up again. There's also a startquest command, but as far as I can tell it does nothing. You'll have to wait up to five seconds for this command to take effect, but when it does, you should get the message that you started Render Unto Caesar. That five second delay caused me to think I was doing something wrong for a long time.
Fix Caesar's Dialog
After I got to the Fort, I tried talking to Caesar, but it just did a weird zoom-in and zoom-out and wouldn't talk to him. This is a bug that has been reported in several places on the internet and the answer is always the same: it's an unsolved bug. Well I'm here to tell you that it's unsolved until now (I think). This seems to happen because every dialog option for an NPC has an associated "condition" which determines whether it's available. If every condition fails, so no dialog options are available for an NPC, the conversation ends immediately and you get that little zoom-in zoom-out effect. Going into the GECK I was able to see that Caesar's dialog options mostly depend on some variables in a quest called "Caesar's Dialog", which is a "hidden" quest. So reset that too:
resetquest 001227a1
Un-hostiling the Legion
Finally, we have to get the Legion to stop shooting at us. We've already set our Legion reputation, but reputation and hostility are actually unrelated in Fallout, rep seems to mostly be used for quest logic. By the way, the Mark Of Caesar item has no effect on hostility either as far as I can tell. So we have to set the enemy status:
setenemy 000ee68a 0001b2a4 1 1
0001b2a4 is the "player faction", i.e. just you, and 000ee68a is the code for the Legion faction. Notice that this is different from the code we used for the Legion faction when setting our rep. This is because of reasons.
