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Rewatching it, I think Twin Peaks: Fire Walk With Me might be Lynch's most challenging film.
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In terms of subject matter, narrative structure, and the (anti-)portrayal of traditional masculine roles in film.
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So, yes, it's uncomfortable to watch. But a film about incest should be uncomfortable. This alienates viewers comfortable with Twin Peaks.
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Also, accepting death, not only philosophically, but as the appropriate and 'right' ending to a narrative is very much not the done thing.