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As it is explained, Chris Higgins (Dana Kimmell) is attacked by Jason Voorhees (Richard Brooker) in some way. All that is seen in the flashback is that Chris is attacked by a mask-less Jason while she is in the woods at night two years before the main events of the film. After a brief struggle, Chris passes out and it is not discussed what happens next. In earlier drafts of the script, Chris was supposed to have been raped by Jason, but that subject matter was removed when producers didn't see it fit for the story-line.
That entire sequence featuring Chris being attacked by Pamela Voorhees while on a canoe in the lake at the end of the film is a dream sequence, following suit of the previous two movies. It was done for the "Last Scare" of the film, while it was also a homage to the original when Jason pulls Alice into the lake.
This movie directly follows the events of "Friday the 13th Part 2", which takes place five years after the events of "Friday the 13th". It is revealed that "Friday the 13th" takes place in 1979, so "Friday the 13th Part 2", "Friday the 13th Part III", and "Friday the 13th: The Final Chapter" all take place in 1984. This would also mean that Chris's flashback sequence would take place in 1982, taking place two years before the main events of the film.
We never actually see Jason in Part 2 without the sack on his head except when he bursts through the window. The end sequence with Ginny is assumed to be a dream or hallucination, and therefore it was Ginny's imagination.
It has been confirmed that the new Deluxe Edition will have both the standard 2-D and the original 3-D version of the movie.
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