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I think in general you want your character to suffer pain, or inflict it. You want to create conflicts where there were none before; not tectonic conflicts but more minor ones. Problems that reveal...
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#4: Attribution notice removed
Source: https://writers.stackexchange.com/a/30587 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#3: Attribution notice added
Source: https://writers.stackexchange.com/a/30587 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
I think in general you want your character to suffer pain, or inflict it. You want to create conflicts where there were none before; not tectonic conflicts but more minor ones. Problems that reveal something about their character (which of course demands you invent something about their character, consistent with what else is known). Most stories are about the obstacles that keep the hero from getting to a position in which they finally can confront the villain and stop their nefarious plan. It sounds like you already have the part about the plot and story arcs, you just need to add some more obstacles that serve to reveal heretofore unimagined soft spots or hard spots in your characters.