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The actor, who played Captain James Kirk in the original TV series and films, had said he was disappointed with the director's failure to come up with a decent part for him in the film.
However, producers are still considering a role for the 77-year-old if they can resolve some difficulties with the plot.
Co-screenwriter Roberto Orci said: "There are two things. One, from our point of view, we are still hoping to find a way.
"Secondly, one of the difficulties that was brought up and discussed with Shatner when we all met him and pitched him ideas is that Trek fans are sticklers for their canon.
"Unfortunately, Shatner's Captain Kirk was killed in Star Trek VII [1994's Generations]."
Leonard Nimoy is currently the only original cast member to have agreed to star in the eleventh film in the franchise.
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