How was Thor allowed to bring Loki and the Tesseract back to Asgard in the first Avengers movie?

Question

At the end of The Avengers, Thor returns to Asgard with Loki and the Tesseract. When Avengers first came out, it seemed that S.H.I.E.L.D. simply allowed Thor to take them; trusting that Asgard would be a better place to both give justice to Loki and to keep the Cube safe.

However, during Avengers: Endgame, we find out that S.H.I.E.L.D. (specifically the Hydra part of S.H.I.E.L.D.) did not want to allow Thor to take Loki; Secretary Pierce specifically tells Thor that they want Loki.

This argument takes place without any changes having happened due to interference from the 2023 Avengers. So it would seem that this always happened in the prime timeline, it was just off-camera in the original Avengers movie.

So given that we now know that S.H.I.E.L.D. was not willing to let Thor take Loki (and I think they wanted to keep the cube as well, though I don't remember if this was specifically being also fought over), how should we interpret the end of Avengers?

I see a few different options:

• Thor eventually won the debate with Pierce and convinced him of his point (unlikely as Pierce was evil).
• Thor simply took advantage of the fact that he is more powerful and took Loki and the cube against S.H.I.E.L.D.'s wishes.
• Someone else—such as Fury—intervened and took Thor's side (also seems unlikely as Pierce outranks even Fury).
• The scene where Thor takes Loki back to Asgard happened some time later, after S.H.I.E.L.D. finished questioning Loki. After all, Pierce did say that Thor could have him when they were done with him.

Looking for either the most likely in-universe explanation that makes sense, or any out-of-universe sources that address this.

Answer 1

We have no idea exactly how much time expired between the capture of Loki, the Tesseract and the return to Asgard and as such there is a lot of wiggle room to allow for a very many scenarios.

For me I believe that it is a combination of your 2nd and 4th points.

Thor didn't consciously use his might to convince S.H.I.E.L.D. to release Loki and the Tesseract as he just behaved he has always behaved based on being the son of Odin and the God of Thunder. Throughout the Thor movies he has always had a sense of just believing that all things would work out and if they didn't they would still somehow succeed, so it is not an arrogance or a Godly expectancy that his word was law, or even a flexing of his powers, it was just that way that things happen for him.

It is possible that S.H.I.E.L.D. did try interrogating Loki but that would be less than useless as does not only Loki believe his Godhood and power make him untouchable he sees humans as so far below him that he wouldn't even bother acknowledging those trying to question him. So there may be some wasted hours pleading with Loki to answer some questions but in the end it would have been a futile process.

And with Nick Fury's answer to the security council;

World Security Council: And the Tesseract?
Nick Fury: The Tesseract is where it belongs: out of our reach.
World Security Council: That's not your call.
Nick Fury: I didn't make it. I just didn't argue with the god that did.

This was made after Thor, Loki and the Tesseract had already returned to Asgard, and it may well be true based on the unconscious will of Thor from above and the comment was more than likely a sarcastic jab at the council.

Answer 2

S.H.I.E.L.D. didn't "allow" Thor to take Loki and the Tesseract. The notion that Thor needed their permission at all is ridiculous. Asgard rules over the Nine Realms and Earth is one of those realms. As the Crown Prince of Asgard, Thor outranks everyone and everything on Earth. S.H.I.E.L.D. doesn't get to dictate terms to Thor; Thor dictates the terms to them.

Even if S.H.I.E.L.D. doesn't recognize Thor's authority, they still don't have the means to successfully defy him. They can protest and demand all they want but unless Thor decides to acquiesce, there is no way they are winning.