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The idea of a protagonist "magically getting super strong" is not one you should entirely throw out the window, depending on the type of story you are telling. Luke "magically got super strong" at ...
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#3: Attribution notice added
Source: https://writers.stackexchange.com/a/35134 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
The idea of a protagonist "magically getting super strong" is not one you should entirely throw out the window, depending on the type of story you are telling. Luke "magically got super strong" at the end of the original Star Wars trilogy, but there were multiple dimensions to what it took for him to achieve that strength and the sacrifices he had to make that made it interesting. Your story is probably (but not certainly / necessarily) going to be more about your protagonist than your antagonist anyways, and so the ability to defeat the villain should be something that said protagonist manages to achieve by some means throughout the story before our eyes.