highly spoiler post:
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He sent Hulkling -- a Kree shapeshifter -- into the headquarters disguised as Tony Stark himself to modify the nanites that were to keep him under control. So, while Hulkling is the one whose fingers did the walking, so to speak, Steve is the one who engineered the plan. Making him responsible for Norman's escape and subsequent attack on the Atlantis embassy. Frankly, that smacks of treason to me. He was in the service of his beliefs, which is fine, but the results of his actions were highly predictable, and it endangered those who were not involved in the conflict. He is, in effect, a terrorist. Honestly I think that's worse than any violation of rights against him.
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Between Cap and Stark's behavior, I'm going to have difficulty reading either of their titles for a long time. I think they've done things that they'll will regret to the point of criminal activity, and they should both be imprisoned for lengthy periods, if not for life. If that doesn't happen, honestly, it kind of ruins everything that has been said in Civil War.