This post may contain SPOILERS.

So I am around 100 hours into Skyrim. At around hour 40 or so I lost Aela The Huntress. While fast traveling with the elder scroll to fight Alduin the first time on top of the Throat of the World, somehow she disappeared. For some reason I did not have a hard save close enough to the point in which she had previously been, so I continued on in the game after reading at work that she would just appear either in my Whiterun house or at Jorrvaskr. I went home to check and wait 72 in game hours to see if she had come back. She did not. She is also not dead as I cannot get anyone else to follow me. Also cannot try giving her to the blades because they already have 3 members. I am now 60 hours further in the game, need a follower for a Daedric quest, and am without the ability to have a follower. So I even gave in to using the command console today to try and find her, just in case she was lost somewhere in the world. I put in player.moveto 0001A697, which is suppose to be her reference id. No dice. It took me to the college of Winterhold with nobody around but me. I have yet to find a single other person who has had this problem. Any advice on how to either get her back or get rid of her? By the way, I have already finished the Companions questline, so I cannot do that trick to get rid of her either. Thanks.

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This happened to me too. After much trial-and-error I have decided the Alduin scripted scene with the elder scroll is broken by having a companion present. 80% of the time the scene just fubars up and Alduin never appears or Alduin accidentally kills both NPCs so they never read the scroll. If you get lucky and it does progress, the companion is forever trapped in that alternate world... her quest-arrow (since she can give quests) is just planted smack on the ground near where you read the elder scroll.

Only fix I ever found was reloading an older save, and that is after spending a good 20 minutes trying to fast-travel teleport her out....