Though maybe there's that one time he refuses and breaks programming, even when the think he's totally broken, because the mission seems so unacceptable to him. Cue worst abuse yet.
What if the target he refuses to kill is a child?
Every part of the Winter Soldier rebels against killing a child: what's left of Bucky Barnes finds it abhorrent, HYDRA's brainwashed and gaslighted puppet doesn't understand how killing a child would be a gift to mankind and shape the century the way Alexander Pierce describes it, and the super-assassin finds it a waste of his abilities when anyone could quite easily kill a child.
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What if the child he refuses to kill is Tony Stark? In the comics, the Winter Soldier went AWOL in 1973 and fled to New York City; what if the Winter Soldier disobeys HYDRA's orders to wipe out the Stark family in 1973 because he comes face-to-face with three-year-old Tony and suddenly all he knows is: CAN'T HURT A KID, CAN'T LEAVE A KID ORPHANED ("Soldier, why did you disobey your orders?" "I-- I don't know. It's just, he... he shouldn't have to get by on his own.") So HYDRA breaks him, freezes him for 18 years, and thaws him to try again in 1991...
Re: Kill or be raped & tortured
What if the target he refuses to kill is a child?
Every part of the Winter Soldier rebels against killing a child: what's left of Bucky Barnes finds it abhorrent, HYDRA's brainwashed and gaslighted puppet doesn't understand how killing a child would be a gift to mankind and shape the century the way Alexander Pierce describes it, and the super-assassin finds it a waste of his abilities when anyone could quite easily kill a child.
+
What if the child he refuses to kill is Tony Stark? In the comics, the Winter Soldier went AWOL in 1973 and fled to New York City; what if the Winter Soldier disobeys HYDRA's orders to wipe out the Stark family in 1973 because he comes face-to-face with three-year-old Tony and suddenly all he knows is: CAN'T HURT A KID, CAN'T LEAVE A KID ORPHANED ("Soldier, why did you disobey your orders?" "I-- I don't know. It's just, he... he shouldn't have to get by on his own.") So HYDRA breaks him, freezes him for 18 years, and thaws him to try again in 1991...