Master S2S: Family
Another memorable moment in the film is the first meeting of The Master (Philip Seymour Hoffman) and Freddie, which in the screenplay is actually their third encounter. In the script, Freddie first sneaks onto the ship and slips on a tuxedo, at which point he first sees The Master and his family in the dining hall. In a controversial scene that was cut from the film, he's drugged by the bartender and passes out. When he wakes up he’s confronted by The Master and their conversation takes on the tone of an interrogation, with the paranoid Master repeatedly asking Freddie if he’s a Russian spy. Freddie is eventually dragged away from this confrontation to sleep it off and when he wakes up from this nap, he meets The Master yet again and this conversation is the one seen in the final film.

Master S2S: Party
In the film, we see The Master and co. arrive by ship at the docks in New York to be greeted by follower of the Cause, Bill White (Kevin J. O’Connor), the man who Freddie gets into a fight with later in the film. In the screenplay, it's revealed that Bill is responsible for the Harley Davidson (seen later during the Pick-A-Point sequence) which he gifts to him upon arrival and The Master rides to the apartment of aging socialite Mildred Drummond (Patty McCormack). In the film, the group enter the fancy her New York apartment and then it cuts to The Master digging into the past lives of the hostess.

In the script, however, The Master first captivates his audience via a lengthy 2+ page monologue where he explains in grand fashion why he finds himself walking with a limp everytime he comes to New York. According to The Master, through processing, he learned that in his past life as “a thief and a criminal” in 1888, he robbed a bank for gold and evaded authorities by escaping into the sewers, only to be faced with a 25 foot alligator. Rather than face the beast, he dropped the gold and escaped but not before shattering his knee in five places. This tall tale ends up coming into play later on in another deleted sequence as Freddie leads a band of men into the sewers to look for The Master’s gold. After this, The Master begins to dig into Mildred’s past lives, at which point he is confronted by “Pig Fuck!” John More (Christopher Evan Welch) who he silences in the script with the more graphic outburst, “Slimy little piece of cum fuck!”

Peggy Dodd’s speech just following the blow-up at the society party is featured almost word-for-word in the screenplay. “WE WILL NEVER DOMINATE OUR ENVIRONMENT THE WAY WE SHOULD UNLESS WE ATTACK.” But on the page, quite crucially it’s The Master who gives this speech while Peggy stands silently by him. By having Peggy deliver this dialogue in the film, Anderson radically shifted the power dynamic of the couple, making it clear that The Master may wear the pants in public but Peggy dominates behind closed doors.

Master S2S: Clark
In the film, Freddie and Master’s son-in-law Clark (Rami Malek) have a very adversarial relationship, with Clark attempting to rat Freddie out as a “spy” and Freddie offering to fart in Clark’s face. In the script however, their relationship is even more complicated. Initially, the pair seem to get along until Clark eventually becomes an antagonist for Freddie. On the way to visit heckler “Pig Fuck” John More, Clark opens up to Freddie, telling him that he’s indebted to The Cause because Book One helped him more than an army shrink ever did. Remember in the film, Freddie shuts Clark down later on by using his own navy service as a measure of his manhood while Clark falls silent, meaning a decision must've been made later on to make Clark not a veteran.

When Clark and Freddie burst into Moore’s apartment to deliver his beating, the script follows the brutality all the way through. Freddie drags John across the floor as John’s wife looks on in horror. Freddie ties up both of them and steals a few valuables before they both flee the apartment. Clark only looks on but does nothing to stop him.

In one of the more interesting deleted scenes in the film, the pair set off to a burlesque club. There, Clark tells Freddie that when he first arrived, people thought he might be a spy, there to steal The Master’s latest book. Clark reveals the secretive nature of the material, saying that all who had read the manual “either went insane or committed suicide.” He says the book contains “the truth about life on this planet” and Freddie asks what something like this might be worth. Clark estimates $25,000 but says the true value is “incalculable.” This exchange is interesting because it indicates that Freddie might actually be interested in stealing the manuscript after all, a charge leveled at him in the film by Clark, which appears fabricated but seems to have basis in truth in this version of the script.

While the pair have this conversation, Freddie ogles a topless dancer, Ellen, who he propositions before passing out. Clark drags him back to his hotel (a sequence glimpsed briefly in a deleted scene) and the next morning, Peggy tries to send Freddie off for good. But The Master steps in and takes Freddie aside to tell him that his son Val (Jesse Plemons) is the one often “finding trouble” and that Freddie should keep an eye on him. After this, Freddie is visited in his room by Master’s daughter Elizabeth (Ambyr Childers) who goes even further in her attempts to seduce him than in the film, planting a kiss on him and dropping her robe to reveal her naked figure.