Playing the game as normal. No mods or anything else are installed so i can get the achievements. I somehow have a follower but they are no where to be found. Deliberately got arrested to see it my mystery follower would show up. No luck. Also tried Vilkas' Purity quest but soon as I walk out of the Companion's guild house to follow him the quest moves down to completed as failed. I was hoping with him the mystery follower glitch would fix itself.

Vilkas' Purity quest seems to get conflicted with his dragon slaying quests. Try slaying the dragon at Skyborn Altar (near Labyrinthian) first before starting his Purity quest. Then see if the Purity quest still gets moved to done as soon as you step out of Jorvasker

Did u tell your Follower to wait for u somewere ?

Nope I have cleared out all my other quests other than the main quest line as Im at the broker a treaty part with the armies and haven't done the civil war questline yet. Brotherhood is done, thieves are done (i regret turning in the skeleton key) so is all the college of winterhold ones.

Pretty sure I had killed that one but I'll check tonight.

Or some of the other ones he typically goes to. I ran into this same issue once, but don't completely remember what I did to solve it. My memory is something about slaying the dragon at one of his typical dragon slaying quest destinations.