Several scenes shot for Star Trek: The Motion Picture never made it into the film.
Scenes with Ilia
After Kirk arrived on the Enterprise and left the bridge for his initial confrontation with Decker, there was a brief scene involving Uhura, Sulu and an alien ensign in which the alien’s loyalty to Decker is established. Uhura observes, “Our chances of coming back from this mission in one piece may have just doubled.” This scene was restored in the longer version (not to be confused with The Director’s Edition).
When Uhura first hears that Lieutenant Ilia is Deltan, she expresses surprise, leading Kirk to respond that the Deltans are so good at their job that “there are no finer navigators in Starfleet, commander.”
Ilia would have been the source of other comments, some of which are heard in the longer version.
Sulu, upon being told by Decker to “take Lieutenant Ilia in hand,” proceeds to act like a schoolboy while attempting to show Ilia the navigation console (with which she is quite familiar). This was supposed to demonstrate the effect Deltan women have on men.
When Decker questions his Deltan friend, she responds by assuring that she “would never take advantage of a sexually immature species,” informing us in no uncertain terms that she has a certain amount of impatience with Kirk for relieving Decker of his command. This is why she has told Kirk about her “oath of celibacy” being on record: she wanted him to know that even if it was not, she would never be interested in anyone who would embarrass Decker in this manner (regardless of Kirk’s reputation where women are concerned). This exchange is present in the longer version.
McCoy beams aboard
Also restored in that version is Dr McCoy’s full entrance, including the yeoman’s observation that “he insisted we go first, sir. Said something about first seeing how it scrambled our molecules.”
In the first version that was shot, McCoy beamed up while carrying a riding crop, indicating that he had been snatched by some Federation transporter without a moment’s notice. This is absent from the available versions.
Just after McCoy’s line about how engineers love to change things, in an unrestored cut, Kirk gazes after the retreating doctor, goes to the wall intercom and announces, “All decks, this is the captain. Prepare for immediate departure.” Had this scene remained as it was, it would have lessened the chances of McCoy’s line being cut (as it accidentally was in many prints of the film).
Also present in the longer version is Ilia’s concern after Kirk summons Decker to his cabin. As Sulu introduces new figures into his console, he must gently remind Ilia to listen to him. After he finishes speaking, Ilia again stares at the door, which leads neatly into the scene in Kirk’s quarters.
Some cuts were put into effect to improve Dr McCoy’s disposition. For example, after Spock comes aboard the Enterprise and is welcomed by Kirk, McCoy observes, “Never look a gift Vulcan in the ears, Jim.”
Spock must have known what kind of an attitude to expect from his old friend because, before the exchange in the officers’ lounge, he asks of Kirk, “Sir, I would appreciate Dr McCoy absenting himself from this interview.” Remaining at the conversation, McCoy causes Spock to show a certain amount of anger, at which point McCoy seriously observes, “If you achieve perfect logic, Spock, you’ll pay a price. It’s given your planet ten thousand years of peace but no poetry’s been written since then, no music.” This comment causes Spock to turn menacingly toward McCoy, until Kirk calls a halt to the situation.
We learn more about Ilia in a sequence restored to the longer version. After Chekov is injured by V’Ger’s energy blast, Ilia approaches him and, through contact with Chekov’s nerve centers, brings about instant relief. Arriving on the scene with a medical technician, Dr Chapel and Ilia exchange friendly glances.
Another casuality of V’Ger’s invading energy probes was not so lucky. When the blinding light probe materializes on the bridge, two security men advanced upon it with phasers drawn and, before Chekov could warn them not to fire, the first man does. In retaliation, the probe envelopes the man in a purple glow. He vanishes, causing the second security man to holster his weapon and Chekov to request that security send no further men to the bridge. This entire sequence has never been revealed.
After Spock’s spacewalk, the Vulcan describes what he has learned, calling V’Ger “a human machine”. McCoy originally commented, “We’re living machines too: protein mechanisms,” and when Kirk observes that V’Ger is trying to find its creator, McCoy asked, “Isn’t that what we’re all trying to do? All us machines?”
The comparison between man and machine led directly to a scene in engineering that was spoken about but not seen in the released version. Decker, taking the Ilia probe on a tour of the facility, hears a message relayed by Kirk:
This is the captain speaking. It appears that the alien ship, V’Ger, is not a manned vessel. It is a living entity, a machine life form. We are attempting to ascertain its intentions. All personnel will maintain yellow alert status.
By phrasing this message as a ship’s announcement, Kirk prevents the Ilia probe from becoming nervous, from realizing that Decker is actually there to “pump” her for information.
Scotty, throughout this sequence, is hostile to “Ilia”, at one point saying, “Lassie, if I were functioning logically right not, I’d be showing you the inside of our metal scrape compactor.”
In a surprising turn of events, Kirk implements a “self-destruct” order to Scotty, in a scene restored to the longer version. In a discussion, Scotty reveals that if there is a chance of destroying V’Ger, a matter/antimatter explosion (which would result if the Enterprise blew up) would be successful in doing this.
Kirk, however, cancels the destruct order in favor of going out and attempting to contact V’Ger directly. This preserves one of the most essential characteristics of Star Trek: a concern for all life.
In a sequence partially restored to the longer version, Spock sheds tears for V’Ger. Still missing, though, is Spock’s regret that although he has found part of what he was looking for, V’Ger “has not… and now, because of what we are planning, will not.” It is this statement that really causes Kirk to cancel the self-destruct order, telling Scotty, “We’re holding off. There may be a chance” (to save Earth, V’Ger and the Enteprise).
Kirk’s original statement at the end, when reporting the “missing status” of Decker and Ilia, included mention of “Security Officer Phillips,” who was vaporized in the sequence discussed earlier.
There were three versions of the movie’s ending. First, the one that’s in the film. Second, one in which Spock has the final line: “A most logical choice, captain,” responding to Kirk’s course heading of “Out there… that way.” Third is a take in which Spock jokes about his need to remain on the Enterprise in order to protect the ship from its erratic, human crew.
Adapted from Allan Asherman, “The Unseen Star Trek (Part II — Star Trek: The Motion Picture),” Star Blazers Magazine