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The villain of the piece
Metaphorical Use
The phrase can be metaphorical, not referring to an actual person but a problematic factor in any situation. 
Not Literal
Doesn't have to be a 'villain' in the traditional sense, like in movies or books. 
Collocation Clues
Words like 'become', 'reveal', 'identify' help to show the function and discovery of the 'villain' in context. 