I'm in the middle of re-reading a couple of stories by Setcheti where the team is betrayed by SHIELD. In one Steve and lured underground in the midst of battle and SHIELD drops a bomb on the sight of the fight, wiping out everyone but Steve, who uses Thor's hammer to call Odin for help. The other story is a Supernatural/Avengers/Night Vale crossover where Tony and Steve are sent on a mission without the others and SHIELD agents try to kill Tony and kidnap Steve. (I'm not telling you titles. Go to Archive of Our Own and read Setcheti's fiction from any fandom that interests you. Wonderful writer!) Okay, my point is that I'd like to find any other stories where the team is betrayed by SHIELD or by the military...even maybe the president. Either an attampt to kill or capture, or even turning them other to another country's government. I can see the possibility of Natasha, Clint, or even Rhodey being pressured by SHIELD or the military to turn on the other Avengers. I'm not counting any attempts by Ross to capture/kill the Hulk.
Which kind of slides right into a hunt for stories where Bucky or Clint are put on trial for their actions when they were not themselves, and the courts/PTB determined to lock him away or executehim no matter what. Do the team protect them, or hand them over? (Steve and/or Nat would fight that, would they?) I just read (and will re-read soon) charmingcontender's wonderful duo or stories Arsonist's Lullably and the expanded version A Flaw in My Code where the team helps Steve Bucky during his trial no matter what. That's something of what I have in mind, but I'd love to see how others would cover the idea.
(FYI, I haven't seen Civil War, so if any ideas come from there, I would know.)