According to the new book The Fifty Year Mission by Edward Gross and Mark A Altman, one of Gene Roddenberry’s early concepts for 1979’s Star Trek: The Motion Picture involved the crew of the Enterprise facing off against a shapeshifting alien that could manifest as biblical figures, accumulating in then Admiral Kirk fighting Jesus Christ on the ship’s bridge. The book quotes Star Trek author and screenwriter Michael Jan Friedman, who had been hired to turn the screenplay into a novel:
“In the climactic scene, Kirk had a fistfight with an alien who had assumed the image of Jesus Christ. So Kirk was slugging it out on the bridge. With Jesus.Gene was – and still is – one of my heroes, for God’s sake. As he had already left the land of the living, this was a unique opportunity to collaborate with him. But when I read the material, I was dismayed … [It couldn’t] possibly have been his best work.”
While this idea may sound radical at first, let’s not forget that the pretty bad Star Trek: The Final Frontier had Kirk and crew facing off against an alien pretending to be God.