Someday I want to write a fic where season 3 of Agents of S.H.I.E.L.D. doesn't take place at literally the same time as Captain America: Civil War (I'd probably have AoS take place after so that Daisy isn't off on the run?) so that AoS isn't busy dealing with Hive during ca:cw and are able to deal with other things.
Because in s3 Hydra is still around and still infiltrating the US government! And the last time they fight Hydra in the modern time is in s5! Plus s4 shows many former members of Hydra turning around and joining another corrupt organization, the Watch Dogs, and they've got a senator on their side! So clearly the government should not be trusted at all because Hydra is still screwing with them! Which is why I think the Sokovia Accords are ridiculous, but that's a topic for another day.
But Steve told Sam and Sharon how he thought it was suspicious that it was conveniently Bucky that "bombed" the UN. Oh no, he's missing, no one cares to search outside of Steve, but if he murders people he'll be found in no time. Oh, and Hydra hasn't been completely eradicated from the world governments yet. Steve obviously had no idea who Zemo was or what his motivations were at this moment, so the obvious answer to him is that the CIA had been infiltrated by Hydra and this all was a ploy to get to Bucky again. And they did it at the perfect time when the Avengers were split by the Sokovia Accords (which very well might have been by orchestrated by Hydra too!) and the public was leaning more and more anti-enhanced individuals. Of course you can incarcerate without a trial or any real investigation, enhanced people are nothing more than weapons and you wouldn't put a gun on trial so why a super soldier? Obviously it didn't end up being Hydra at fault but it makes sense why Steve could think that, especially since the next time he sees Bucky he is in Winter Soldier mode!
Now imagine S.H.I.E.L.D. seeing this crap. They darn well know that Hydra is still out there and still within several governments. And they very well could make the same assumption Steve made. Also they potentially know for a fact that Bucky didn't bomb the UN. You know how S.H.I.E.L.D. kept an eye on Bruce pre-Avengers but kept their distance while keeping everyone else off his back? Maybe they did the same thing with Bucky so they know dude never left Bucharest. But it's in their interest to make sure Hydra doesn't get their hands on Bucky again.
So now I'm just imagining S.H.I.E.L.D. just showing up and breaking Bucky, Steve, and Sam out. I haven't worked out exactly how I'd want it to go but I'm imagining that similar to how the US government created the Alien Threat Containment Unit that kind of replaced S.H.I.E.L.D. in handling alien threats, they probably had something similar that was meant to weed out Hydra. So they come posing as members of this anti-Hydra unit and basically straight up tell Ross their concerns of how darn easy it would be for Hydra to exploit Bucky again and say that they have to do an investigation (because the CIA is doing every atrocious thing possible to screw over Bucky, certainly is starting to look like that Ross could be affiliated with Hydra) and that they will protect Bucky both from Hydra and blatant human rights violations.
Obviously Coulson can't show up because of Steve, Tony, and Natasha being there, but he's nearby with the quinjet ready to help if needed. But I'm imagining many of them being there. May is the one they say has to stay with Bucky (because she's the Cavalry. Natasha, Steve, and Sharon know who she is. Everyone trusts her ability to fight off Hydra/fight Bucky). Koenig would be there as like an administrative person (okay but what if both Sam and Billy are there but they both go by the same name and are never in the same room together? So then they can be in two places at once, finding ways to get out? I like it). Daisy could be there as the person who investigates the computer system (and also ends up hacking to get them out of there). Clearly Hunter can pull off being a lawyer so he can do that again (is it again if this before s5? lol). On that same note, Bobbi's already pulled off being an investigator of spies in Hydra before so I think she could investigate Ross specifically which would distract the leader and keep the facility more open to escape. That actually would be one heck of a resume for her to say that she pulled an Uno reverse card on Hydra and infiltrated them. I haven't figured out what FitzSimmons and Mack could do, but I'm sure there's something they could do that is scientific/mechanic. Or they could also be investigating. Actually, one of them has got to be near Sam and Steve so that they can get them out of there too.
Anyway, their plan works and they manage to get Bucky, Steve, and Sam out of there while dropping evidence that Zemo had infiltrated the CIA. Not just there. But Daisy drops it online. So everyone knows that Bucky was framed and the CIA didn't even bother to investigate whether he actually did the bombing or not. But they all get out of there, Steve learns about Coulson, Zemo gets arrested. This whole thing severely damages the Sokovia Accords' reputation and people start pushing back against it. And Bucky, Steve, and Sam keeping hanging out with S.H.I.E.L.D., and eventually tons of the other Avengers join them since the government starts doubling down (to which S.H.I.E.L.D. keeps responding in similar fashion).
Idk, I think it could be a fun fic to write.
