Campaign director Jason Blundell said Treyarch took inspiration from Mass Effect's hero, Commander Shepard, a character who can be played as a male or female. The overall script for that game didn't need to change to accommodate a player's gender--and Black Ops III's won't, either.
According to GamesRadar, Treyarch Studios head Mark Lamia described Black Ops III's story as being "gender neutral." He also referenced the script for Alien, which was originally written for a male to play the lead role before Sigourney Weaver ultimately got the part. "The emotions and dynamics between characters is kind of gender neutral," he said about Black Ops III's story.
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