I've looked around for an answer to this, but can't find much. As the title says, I can't join the Companions, because whenever I get out to the courtyard to train with Vilkas right at the start, first he'll stand there and yell at me about not using magic (despite the fact that I'm not wearing anything enchanted, and have nothing equipped except unenchanted armor and a sword). He'll draw his sword, put it away again and continue on about magic, then he'll finally tell me to come at him. I whack his shield a few times, and then he and every single Companion becomes hostile and tries to kill me.

After several reloads, I manage to get through the training and he gives me his sword to take to Eorlund. Halfway there though, right about when I pass the entrance to the Underforge, all the Companions once again try to kill me. Eventually I just started a new game with a clean save and tried then. Somewhat successful, I'm on my way to Eorlund with the sword, then out of the blue Vilkas turns hostile again and starts trying to punch me to death. It takes a minute, he'll talk with me and I'll walk some distance away before he turns hostile, but at least this time it's just him and not the others as well.

I got the game around launch, so for well over a year I've never encountered this problem until very recently. I've installed and uninstalled a number of mods, but none have ever affected the Companions or their area in and around Jorrvaskr, unless you count Dawnguard with its werewolf upgrades.

So any ideas? Any help with be much appreciated!

You can try the suggestions in the bug section http://www.uesp.net/wiki/Skyrim:Take_Up_Arms.

Also make sure you haven't got a bounty in any hold.