Actions of making something clean or removing unwanted things; in baseball, a batter's position that comes after three players have already batted.
From clean (to make free from dirt) plus up (adverbial particle) plus -s (plural). The baseball sense comes from the role of cleaning up the bases by batting in runners.
In baseball, the cleanup hitter is usually the best player on the team—not because of actual cleaning, but because they're responsible for 'clearing' the bases by getting hits when other runners are already on base. It's a great example of how sports create their own slang from vivid metaphors.
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