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A written prologue that opens the film states that the story was based on "authentic records of the year 1692." According to the film's pressbook, the sermon preached by Rev. Samuel Parris was taken "almost wholly" from a rare collection of sermons by Reverend Deodat Lawson, who served with Parris at Salem Village. As reported in the pressbook from information found in the Essex Museum in Salem, in Puritan days, there were two Salems: Salem Town, on the seacoast, which is now modern Salem; and Salem Village (now called Danvers), a farming community located seven miles inland, where most of this film is set. The film was shot on location on a farm four miles outside of Santa Cruz, CA, where Paramount reproduced the Salem countryside on forty acres of land. A sailor's shanty was built on a bluff overlooking the Pacific Ocean at Carmel, CA. According to the pressbook, the British Museum supplied two ancient songs for the film: a sea chanty written in 1530 and a ballad, "Bid Me But Live," ca. 1630, which was sung by Fred MacMurray in the picture. According to a January 26, 1937 news item in Hollywood Reporter, an eight-hundred foot trailer was being prepared featuring director Frank Lloyd in the cutting room. "Action" scenes shot through the Moviola were also included.
According to files in the MPAA/PCA Collection at the AMPAS Library, on May 14, 1936, Joseph I. Breen, Director of the PCA, wrote to Paramount distribution executive John Hammell with his reaction to an outline of Bradley King's story, which was called "Between Two Worlds." Breen requested that Hammell have his research department verify whether alleged witches were actually burned in Salem. Breen wrote, "It is our impression that there were no burnings-rather was the alleged punishment confined to hangings." The film's program included the following note: "The widely held belief that there were witch burnings doubtless arises from witchcraft annals in England and France (most notably Joan of Arc) where there were many burnings. This, however, was never true in America." In reference to a kiss between Roger and Barbara, the PCA cautioned the filmmakers in a letter dated August 27, 1936: "they should, of course, not be lying on the ground." Further caution was expressed about the portrayal of the clergy: "While there is of course ample historical grounds to prove that many of the clergy were caught up in the hysteria of the time, it might be well to counter-balance this in your picture by introducing briefly another minister [besides Reverend Samuel Parris] who will typify the more rational element among the clergy." On August 28, 1936, Breen wrote to Hammell, quoting the Production Code, "Ministers of religion in their characterizations of ministers should not be used in comedy, villains, or as unpleasant persons," and warning Hammell to "make definite changes in your script RE: Rev. Parris to bring picture in compliance with above Code provisions." An inter-office memo dated August 31, 1936 from Geoffrey Shurlock, Breen's assistant, outlines Hammell's response to the previous letter. The memo states: [director Frank] "Lloyd aware of danger in portrayal of the minister. Rev. Parris, played by [Ivan] Simpson, will portray him as stern upright minister, but with no tinge of the blue nose about it. They are also cutting out most, if not all, of the scenes in which minister is shown (in script) actually connected with the witch-hunting. [They also will be] introducing the character of another minister who will represent the liberal viewpoint, and who will protest against the witch-hunting hysteria of the time."
According to a news item in Hollywood Reporter on December 29, 1936, following a sneak preview of the film, Paramount decided to revise the ending, and recalled the company back for a few days of retakes. A script dated October 15, 1936 in the Paramount Script Collection at the AMPAS Library indicates that in the preview version, after Roger saves Barbara from being hanged, Sewall calls an end to the witchhunt, and Barbara collapses into Roger's arms. Elder Goode then realizes Virginia has lied, and Sewall prays to God for forgiveness. A member of the mob then calls for the burning of the tree at Gallows Hill, and the film ends. In the script to the revised final reel dated December 29, 1936, the governor signs a decree abolishing the trial for witchcraft and orders the tree at Gallows Hill to be burned. (The signing of a proclamation that freed prisoners of the witchhunt appeared in an early script, but had been removed by 1 September 1936.) Later Barbara emerges from her dungeon cell, where she embraces Roger. The tree is then burned. In an early script dated August 22, 1936, John is struck by a soldier while defending Barbara at her hanging and dies. According to contemporary news items, this film was screenwriter Howard Estabrook's first producing assignment for Paramount. Some reviews erroneously credit Russell Simpson as "Rev. Samuel Parris." Russell appears as "Village marshal," and Ivan Simpson appears as "Rev. Samuel Parris."