I am playing a new game, level 6 I think. There I am running east across the icy wastes after I did a DB hit in Dawnstar. The law is on my case so I am putting some distance between me and them.

My pursuers had disappeared from view so I started taking it easy. A guy looks like a bandit is walking towards me.

My sword is sheathed. He attacks! I hit back. I am besting him when I realise this bandit is Vilkas.

I had been planning to join the Companions. If I kill Vilkas the Companions would be ruined. I don't know if he is immortal or not but I didn't dare try to find out.

I sure don't understand why he wants my death. I've never been inside Jorrvaskr and I am only doing some jobs for the Jarl's steward in Dragonsreach. Have done nothing else in Whiterun. Maybe someone has asked the Companions to do me in but why? Don't they like the Dark Brotherhood's assassins?

That's a new one on me. I've seen Vilkas when he's hunting in several spots around Skyrim, but he's never attacked me. Is it possible you killed Ria or Farkas or somebody else in the Companions without realizing it?

The companions have all started to attack their Harbinger (me) on sight after I turned into a vampire. They don't attack me when I visit Jorrvaskr though, it's weird.

I am using the 1.4.21.40 beta patch. Like I said, I've had nothing to do with any Companion members or Jorrvaskr. I've only just started a new game. Never met any of them before in this play-through. I've only killed bandits for the Jarl's bounty given by the Steward. I killed Grelod and a couple of Nazir's DB contracts. That's all. This is weirder than weird.
I suppose when I do walk in to Jorrvaskr, Vilkas will behave like a good guy. If they want to kill me in Jorrvaskr then I will not be able to join the Companions.

It may be the typical random psychotic episode syndrome case that occasionally afflicts wandering NPCs. I haven't had any trouble from Vilkas or any of the traveling Companions, but Louis Letrush, Talsgar, and one Riften guard have gone ape-guano on me. I don't count the expected hostiles that randomly show up to run me down and cut me up, like members of that pirate clan, the Horkers, I think they're called. Oh, and the random and very angry Argonians.

Vilkas, is a companion and the companions are under the same scripting as guards that is why he attacked you because you have a bounty on you. Down side is they will not attempt an arrest just try and kill you, so the only option is to out run them. Unrelenting Force is great for those that you dont want to kill as by the time the get back up you can be long gone.

How did you become a vampire with the immunity to disease you get as a werewolf? Did you cure yourself first? lol

The Companions are sworn to protect Tamriel, my guess is that outside the walls of Jorvaskr they see you as a threat? Funny when they used to be one, too... heh. I've never been attacked by them anywhere, I have run into them in different places where they were hunting or just "traveling" together, though.

Yeah I cured my lycanthropy as my first official act as Harbinger, shortly thereafter I got turned into a vampire. Those companions are hypocrites. It's okay to flip out and turn into an ugly manslaying werewolf, but I guess becoming a fairly innocuous looking vampire is where they draw the line. They came at me with the typical anti-vampire spiel, with Vilkas going, "Your kind doesn't belong here!" and Ria gleefully shouting "Burn it! Burn the vampire!" Way to make me feel welcome, guys.

I CALL SHENANIGANS!!!!!

strange. They're not supposed to, since you have a high/max level of "friendship" with them. They shouldn't even care.

Yeah it's weird, they only attack me when I'm out in the feild. I managed to talk to Farkas ("You've been a good friend to me, that means something") for a few seconds before the group went hostile once, but everytime I encounter them outside they end up attacking. I just turn ethereal and run away.

hmm... perhaps curing yourself of lycanthropy reduced the "friend" rating?

shouldn't, well maybe with Aela but not with Farkas or Vilkas

Aela is my wife. I keep her locked up in Hjerim so she won't hurt herself (accidentally Marked for Death her [what is the verb on that?] a few times in Ysgramor's Tomb). She never attacks unless I go stage four vampire, but that can be said of most NPC's. Maybe the companions are mad cuz I took away their resident hottie and left them with super [censored] and.. well... Ria...

hmmm... well, hard to know for sure. if you're on PC, I'd consider loading an old save as werewolf and become a werepire to test it.

Nope, PS3, I don't mind it though. That character isn't really very loyal to the companions anyway.

that might do it. I hear Skyrim seems to have the most issues on PS3 over the other platforms.

one word. MADGOD!!!!!!!!!!!!!!!!!!!!!!!!!!!!

(honestly its not just PS3 i had that problem before on the 360)

My only bounty is 40 gold in the journal for Dawnstar for hitting Beitild — there were no witnesses. Is that enough to anger the Companions? I guess a return in a few days to Dawnstar and paying the fine will fix it. I have no dragon shouts yet because I've not started up any dragon quests with Farengar Secret-Fire or Jarl Balgruuf.

yeah 40 gold is enough to trigger the companions and some guards, guards can be funny though some dont seem to care others I think I out for a promotion.

After I became Harbinger of the Companions, completed Aela's radiant quest, did the daedric quest for Hircine, and walked into the hall the entire lot briefly became hostile, then went normal. I was in the area transition between the upstairs and sleeping quarters. Immediately before I had an altercation with a guard outside of town during a dragon attack (stray blade = assault & invoked thane status). I broke out of the conversation, and ran and fast travelled. I never went near the Jarvasskr again. I decided to get married. Farkas "arrested" me at my wedding and followed me with his two handed sword drawn. He would fight anything that remotely was hostile to me. But I could not fast travel because "guards were chasing me". From that moment on Farkas behaved as a Companion Friend AND a Hostile Whiterun Guard. I could not fast travel. I cured him. I tried to kill him. I ran and jumped down mountains, and used Whirlwind to travel, and I'd think I'd lost him. He'd reappear in the middle of sneaking through a pack of Falmer "now you I like." and of course the giant Charlie Foxtrot complete with poison and reload, whereupon he'd be right next to me. Then, I'd try to dismiss him, and he'd re-arrest me. I could not get rid of him. So ended one 154 hr playthrough.

My current playthrough I've gone through the werewolf ceremony and haven't been back to the lodge, and honestly I don't need to go back there. I've already got the Harbinger achievement.

I'm on the 360. If I were on the PC, I'd have unchecked "Companion" from his identification at this point. Then dismissed him. If he failed to leave, I'd just go back into the console, uncheck essential, and type "Kill".

I guess reverting to the save before that dragon attack would've resolved all this. The guard wouldn't have accidentally been hit and then there would be no hostility.

He is actually part of the guard faction, though it is whiterun guards...

That was like 6 hrs earlier, and I got mad. So I moved the save to the cloud and started over. Like an idiot I'd been relying on autosaves, but I did end up doing some things a bit differently this time and a bit more chaotically with RPing with much less metagaming. Perhaps thats why things turned out worse for the current character at least concerning black marks on the soul.

With factions what I've learned is that pulling the "I belong to the thieves guild" and "thane" crap doesn't clear your rep with the town guards. They always get you the next time. That bribe is probably more than they make in several years, and taking a second one would be too obvious to their comrades. I mean why did I even bother pulling the Thane crap over a 40 gold fine anyway? Probably because I was thinking that I helped save their lives. It reminds me of the number of times I've killed myself in CoD HC "ricochet" when some idiot runs in my line of sight just when I'm firing "friendly fire will not be tolerated".

I have a minor version of the OP's problem. When he sees me, Farkas draws on me, then says "You've been a friend..." and I can engage him in dialog, including getting training. He doesn't attack me, he just wields his two-hander. The nuisance is that he engages me in conversation as soon as he gets close enough, and repeatedly, so I can't get anything else done around Jorrvaskr if he's nearby. As mentioned above I can't fast travel because "...guards are chasing you." Fortunately I'm faster than he is, so I can outrun him and eventually fast travel. The other Companions are fine . . . if Farkas is elsewhere.

I was very puzzled when this first happened, and then realized that it must be because I have a bounty in Markarth. It's just a tiny bounty , something about slaughtering every guard in the city after a couple of them tried to frame me and then attacked me. The good thing about it is that every time I visit the Reach I collect a lot of saleable armor from the guards and bounty hunters who come after me. Actually, there are so few guards left in Markarth that I can fast travel into the city, do my business, and then leave with only a couple of more dead guards each time. It's nice that no one else in the town cares as I kill the guards right in front of them.