3) “The Scorpion”
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This one isn’t a storyline as such, but The Scorpion’s first appearance from way back in the 1960s could very easily be adapted for Spider-Man: Homecoming.
Mac Gargan was a private eye hired by J. Jonah Jameson to discover the hero’s secret identity, but the newspaper publisher ultimately decided to fund an experiment to transform him into The Scorpion when that plan failed.
Unfortunately, Mac was driven mad in the process and ended up going after both Spider-Man AND Jonah, something which forced Peter to save the guy who created one of his greatest foes.
An adaptation like this would establish JJJ and The Daily Bugle as an antagonist of sorts to Peter, and The Scorpion is most definitely a very cool bad guy from a powers/visual perspective.