Cook bacon in a large nonstick skillet over medium-high heat until crisp, about 6-8 minutes. Transfer bacon to paper towel-lined plate and pour out all but 2 tablespoons rendered fat from the skillet.
Pat scallops dry with paper towels and season with salt and pepper. Cook scallops over medium heat in the rendered bacon fat in skillet until golden brown, about 2-3 minutes. Flip scallops and cook until firm and almost opaque, an additional 1-2 minutes. Transfer to a plate and tent with foil.
Add onion and garlic to the skillet and cook until softened, about 3 minutes.
Add corn, lima beans, tomatoes, and jalapeño pepper and cook until heated through, making sure to stir frequently, 3-5 minutes.
Add butter to skillet and stir until the butter is just melted.
Remove the skillet from the heat and stir in the chives and bacon, season with salt and pepper to taste.
Serve succotash on plates and top with sea scallops.