#now i want to write an au where he isnt sent to asgard and hydra gets their hands on him

[lokigodofaces]

I realized this while I was writing one of my fics, but it doesn't really work into any of my current fics and I still want to scream about it to people, so that's what I'm going to do here.

In Endgame, Pierce tries to stop Thor from taking the Tesseract and Loki to Asgard. Thor tells Pierce that Loki will answer to Odin for his crimes, and Pierce says Odin can have "what's left" after Loki answers to S.H.I.E.L.D. That specific line got me thinking, because it sounds ominous. "What's left" implies that Pierce intends to torture Loki or something similar. Which got me thinking, because we know that Pierce is actually Hydra.

From our knowledge of Hydra in the movies and Agents of S.H.I.E.L.D., there are a few trends we see. 1) Hydra has an obsession with anything alien (Tesseract, scepter, diviner, Inhumans, monolith, Hive). 2) Hydra has an obsession with experimentation with the aim of creating super soldiers or some other form of enhanced individuals or anything similar (Red Skull, Bucky and other Winter Soldiers, Centipede, Deathlok, Scorch, scepter, Maximoffs, Jiaying, Whitehall, diviner, Lincoln, Inhumans in general, Ruby). 3) Hydra does this experimentation to create human weapons they can control to some degree (Bucky, other Winter Soldiers, Maximoffs, Deathlok, Centipede, Scorch, Inhumans, Ruby).

So there's a very high chance that Pierce intended to send Loki to be experimented on. While we can't know for certain what would happen, I can give a few guesses.

From AoS and the films we learn there are a few main people in Hydra that are particularly connected to human experimentation. Arnim Zola, Raina, Ian Quinn, Daniel Whitehall, Doctor List, and Wolfgang von Strucker.

Zola is dead at this time, but his mind was converted to an AI. Zola was the main person involved in the Winter Soldier program. We don't know much about most of the Winter Soldiers, but it looks like they weren't really used on any missions because they were unstable, and we don't entirely know who was involved in the experimentation that made them. Because they were ineffective and we don't know their names, I'm going to assume they don't matter much anymore. Zola would then be involved with Bucky and Project Insight. In Winter Soldier we learn he made the algorithm for Project Insight (which would launch in just two years), and if we treat What If...? as canon*, there is a Zola unit in the same building Bucky was kept at. Since those are the only two things we really know Zola was involved in with experimentation, and he's kind of dead at this point, I would say him being involved with anything with Loki is a low possibility.

Raina and Quinn are actually not Hydra. Raina worked with Hydra for a bit as a means to her own ends, as was Quinn. They were working primarily for John Garrett. They worked on the Centipede project and Deathlok project mainly. They both would have been very interested in Loki I feel. But Quinn doesn't really have the background to do anything with Loki or the scepter. With Raina, she wouldn't be interested in experimentation. She worked with Hydra specifically to learn more about Inhumans. She knew Inhumans were created by aliens that were described as blue angels. Perhaps Loki would know something. But, as I said, neither are actually Hydra, just consultants. I don't think Hydra would send over an alien weapon with the power of mind control and an alien from legend to two people that can't be trusted in the same way as an actual member of Hydra.

As for Daniel Whitehall, he has a very specific thing he's looking for, something not connected to Loki. He found the diviner and Jiaying, now he's mainly interested in Inhumans. Since Loki isn't Inhuman and there isn't any known connection between him and Inhumans, I don't think he'd particularly care about anything related to Loki, other than to maybe ask for some reports if any connection is found by anyone else.

Which leaves List and Strucker, who work together a lot. We do know from Winter Soldier, Age of Ultron, Agents of S.H.I.E.L.D., and Endgame that they are connected to the scepter. The scepter was sent to List, and he worked with Strucker on the scepter and on the Maximoffs, who were experimented on with the scepter. Since they had the scepter, it would make sense they'd get Loki. We also know that they didn't really have an area they were more focused on than others. You're enhanced in some way or alien? Congratulations, you caught their attention. They experimented on the Maximoffs (as well as several others that went through the same experiment and didn't survive), Lincoln (who they didn't know was Inhuman at the time), Mike (some guy with lots of prosthetics), and on the scepter. Why not throw Loki in as well?

As for their track record, like I said, most of the people we know about that they experimented on died. If it weren't for Daisy, Lincoln would have died. And Mike was not in good shape when S.H.I.E.L.D. rescued him. So, I can't say exactly what would happen, but I can confidently say that Loki dodged a bullet.