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I always thought that the ending of the movie, with the female scientist on the plane, was a coincidence, and in line with the dystopian view of the movie in general. It makes sense that some random insurance salesperson who happens to be in the same place as where the virus spread, just happens to becomes one of the powerful players in the post-apocalyptic world.
However, the IMDB FAQ page (http://www.imdb.com/title/tt0114746/faq) shows (without sourcing) that director Terry Gilliam intended the ending to be happy, which would nominate this movie as an entry for Word of God.
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