(written from a Production point of view)
A deleted scene is a filmed segment of a movie or television episode which was removed from the final product for any of a number of various creative reasons. Among the most common reasons for a scene to be deleted are time constraints (a scene could make the film or episode run too long) and narrative pace (a scene could slow down action of the story).
A deleted scene could also be replaced with another scene, in which case the scene deleted becomes an "alternate scene." A scene may also be merely trimmed down, again either for time or pace. In this latter scenario, the full version of the scene is known as an "extended scene."
In its history of 716 episodes and twelve films, Star Trek has had many scenes removed or entirely replaced. Examples include what would have been the opening sequence for Star Trek Generations – in which Captain James T. Kirk is orbital skydiving – and a scene in Star Trek Nemesis in which Martin Madden replaces William T. Riker as the first officer of the USS Enterprise-E.
Examples of deleted scenes
Star Trek: The Original Series
- "The Cage"
- At the beginning of the scene involving Vina acting as a Orion slave girl, the Talosians are seen speaking through a trader and an unnamed Starfleet officer, trying to induce Captain Pike to accept their "gift" of an illusory life as breeding stock. Moments later, Vina threatens another servant who pays too much attention to Pike.
- In the scene following, set in the transporter room, Number One reiterates the danger of the rescue mission and its voluntary nature. There was dialog filmed but cut from the final print where Number One addresses Yeoman Colt. In it, she points out that Colt is new to the Enterprise, hinting that the yeoman need not join the landing party. Colt responds by saying that she has been trained as any other member of the crew and that she was Captain Pike's yeoman. (The Making of Star Trek, )
- An alternative, pre-broadcast edit of this episode exists, which amongst other differences includes a few scenes and extended scenes that were cut for the final broadcast version. 
- A filmed, but deleted shot shown Kirk saluting the Romulan commander before he destroyed his ship. A scene showing the commander and Decius arguing about the Praetor's orders, soon before the centurion died, was also filmed, but cut from the finished episode. 
- Two shorter scenes were filmed, but cut from the final episode (possibly due to time). In the first, crewmembers are watching the performance of Hamlet on the bridge. In the second, Lenore Karidian is shown resting in sickbay after her mental breakdown. 
- A scene of Ben Finney meeting his daughter, Jamie in engineering, after being beaten up by Kirk, and confessing where he damaged the ship's systems was filmed, but cut because of time. It was replaced by a captain's log voiceover, explaining what happened. 
- A conversation scene between Anan 7 and Sar 6 in Anan's quarters was filmed, but cut from the episode. 
- A scene showing Spock and Leila walking and romanticizing by a stream was scripted and filmed, but cut from the finished episode. However, it appears in the episode's preview trailer. 
- A scene filmed, but cut for time included Peter Kirk visiting the bridge after his recovery from the alien parasites, wearing a child-sized version of a command division Starfleet uniform with lieutenant stripes, and sitting in the captain's chair. It is also revealed that instead of moving back to Earth to live with his grandparents, Peter is going to be adopted by a colleague of his father, and stay on Deneva. After Peter leaves, Scotty tells Kirk, his nephew shall go to Starfleet Academy. Kirk replies that he hopes he won't, not wanting him to face a similar decision like he just had to make. 
- Another scene that was filmed for "Operation -- Annihilate!" involved Spock, on the surface of Deneva, immediately after having rendered the club-wielding Kartan unconscious with a Vulcan nerve pinch. Kirk reprimanded Spock, via communicator, for the lateness in reporting in, a delay accounted for by the attack, and a spasm of pain then caused Spock to realize that the parasite within him might be in contact with the others of its species. (Star Trek Magazine issue 163, p. 32)
- A scene filmed, but cut from this episode featured a team of security guards, ready to beam down to Pyris VII, but are unable because of Sylvia's invisible force field surrounding the Enterprise. 
- "I, Mudd"
- A short scene, featuring Enterprise crewmembers playing games and being entertained by the Mudd androids was filmed, but cut from the episode. 
- An extended scene was shot in the newly-built recreation room for "Elaan of Troyius" that was never aired. In it, Kirk, McCoy and Uhura are first amazed to see Spock tuning a Vulcan lyre, and then impressed to learn that Spock placed second in the all-Vulcan musical competition – Sarek took first prize. Hearing Spock play the lyre, both Uhura and Kirk were struck with an idea for preparing the Dohlman for the impending nuptials.
- The course in etiquette was cut short when the Dohlman knifed her teacher, Ambassador Petri, and Kirk was anxious to successfully complete the mission as the Federation High Commissioner was to attend the wedding. In that regard, Kirk asked Spock to play a love song – Spock referred to it as a mating song – that would be piped into the Dohlman's quarters as Kirk resumed the lessons left off by Petri.
- The results were less than salutary. The scene continues in Uhura's cabin (which she surrendered to the Dohlman), and Kirk watches in disgust as the Dohlman eats in the manner of Henry VIII. From this point forward, the scene as filmed is shown in the final print, with the exception of the Dohlman's agitated query about "that sickening sound" filtering into the room. Naturally, the music Spock was playing is not part of the soundtrack.
- The final revised shooting script was completed on 27 May 1968 and the scene was shot on 10 June 1968. 
- A short scene near the top of the fourth act where Sulu threatens Kirk with a phaser. 
- Two scenes were filmed but cut from this episode: in the first, Scotty uses McCoy's computer in sickbay to find out how to make Spock ambulatory. In the second, the mechanically moved Spock is brought to the bridge by McCoy and Scotty before the landing party beams down to Sigma Draconis VI. 
- Also, an ending scene on the bridge (with an apparent pun to end the episode) is present in the final draft script. It is unknown if the scene was filmed and cut from the finished episode, or it was scrapped entirely. 
- A scene featuring John Buonomo as an orderly was apparently cut.
Star Trek: The Animated Series
- None listed as of yet.
Star Trek: The Next Generation
- While "on board" the alien lifeform, tentacles reach out of the wall and grabbed for Deanna Troi and Riker. The producers decided these special effects looked horrible and removed the scenes from the episode. wbm
- A scene including guest actor Michael Rider as the transporter chief was cut from the final aired episode. Rider's name remained in the credits for the episode.
- Several scenes were filmed but later cut from the episode during editing. These scenes came to light in March 2013 when a Trek collector uploaded the contents of an early workprint VHS of the episode to the internet. . See the episode page for more information.
- A scene where Wesley Crusher convinces Data to talk to Worf on his behalf, as Geordi La Forge protests. (Included on the TNG Season 2 Blu-ray release.)
- A scene, in which Annette and Eric asked Wesley Crusher to accompany them on a holodeck ski trip, involving a conversation in a corridor and dialogue for both guest actors, was removed due to time's sake. Both guest actors appeared briefly in a crowd scene at the end of the episode, but received no credit, nor did they speak. (Star Trek: The Next Generation Companion) A scene which featured Annette in sickbay after she broke her leg, was also removed from the final aired episode. This scene would have also included a larger part for guest actress Mary McCusker, who played a nurse, who treated Annette and was hit by an energy burst from the malfunctioning replicator. 
- A scene which involved Raymond D. Turner as an Enterprise-D teacher was cut from the aired version. 
- Two scenes were cut for time, from the episode's final edit, one of which was a secondary interrogation scene showing Admiral Alidar Jarok being questioned. (The Official Star Trek: The Next Generation Magazine, vol. 20, p. 33)
- A scene was cut from the final version of the episode which includes Brandi Sherwood as a command division officer who assisted Wesley Crusher in rescuing his mother. (BRAVO, 1989)
- Stefan DeSeve was in his quarters trying to use a replicator to get some coffee. However, he had spent so many years living among Romulans that he had forgotten much of his native language, and had difficulty remembering how to actually pronounce the word. (Star Trek: The Next Generation Companion)
- A scene where Fajo sends Varria to test Data's sexual abilities (in which Data references his only sexual encounter from TNG: "The Naked Now"), however, Data learns of Fajo's intent, leaving Varria utterly humiliated which would later fuel her desire to betray Fajo in the climax. 
- A scene in which Dr. Crusher talks to the wife of Dr. Richard Hill, who doesn't remember her husband. 
- Several scenes were filmed but later cut from the episode during editing. These scenes came to light in March 2013 when a Trek collector uploaded the contents of an early workprint VHS of the episode to the internet. . See the episode page for more information.
- Scenes 12-14 were cut from the final episode and would feature a conversation between Worf, Dr. Crusher, and Simon Tarses in sickbay. According to the call sheet from Friday 22 February 1991 it would include 1 5/8 script pages.
- A scene involving a morgue attendant, played by Van Epperson, was removed from the final episode. This scene was according to the script scene 3.
- A Ten Forward scene featuring Riker, La Forge, and Troi was cut out of the beginning of this episode. In this deleted scene, the three of them were speaking of the rogue comet that came in contact with the Enterprise in 2370. Riker is a little annoyed when he receives a snack and drink which he did not order. Troi takes a bit of the snacks, and likes it. La Forge scans the drink and discovers it to be blood. Riker wants to talk to the bartender but La Forge insists that it might not be his fault.
- A scene with Troi going into her quarters and beginning her bath session in her on-duty uniform was cut out of this episode.
- A scene including Martha Hackett as Terrellian pilot Androna who appeared in the Devron system was filmed, but cut from the aired version. The costume worn by Hackett was sold off on the It's A Wrap! sale and auction on eBay. 
Star Trek: Deep Space Nine
- A scene in the script that was filmed but eventually deleted featured Sisko meeting with Kai Opaka for a second time, so as to return the Orb. He tells her that fourteen planets have contacted the Federation to open trade links through Bajoran space. He tries to tell her he believes the Prophets to be wormhole aliens, but she tells him she does not wish to hear. Opaka tells him "that is why a disbeliever was destined to seek them – one should never look into the eyes of one's own gods." (In the first season finale "In the Hands of the Prophets", Vedek Winn, speaking to Commander Sisko, quotes this line from the deleted scene.) Opaka also tells Sisko that his journey is only just beginning. Rick Berman commented, "There's a wonderful scene where Sisko goes back down to Bajor to return the Orb to Kai Opaka that we took out. Cutting is horrible, especially when it's something so close to you as the pilot was." (Captains' Logs Supplemental - The Unauthorized Guide to the New Trek Voyages)
- A scene was filmed for this episode with O'Brien singing "The Minstrel Boy" while being chased on the runabout; an allusion to the TNG episode "The Wounded", where he says it is his "happy thought" song for bad situations. However, due to a continuity slip that wasn't noticed until the last minute, the scene was removed. The mistake involved the name of the pursuing runabout, which is referred to as the Rio Grande. However, the Rio Grande was the runabout being chased. The pursuing ship was actually the Mekong. This mistake wasn't noticed until writer Paul Robert Coyle was sent a copy of the shooting script, which is only sent out after an episode is completed. By the time the mistake was spotted, it was too late to sort it out, so the scene was simply removed. (Star Trek: Deep Space Nine Companion)
- The relationships between Kira, Dukat, and Damar were further explored in a scene filmed but cut for time. After Kira calls Dukat an interstellar tyrant, Dukat retorts that he prefers the term "despot". Dukat proposes to assign Damar to escort Ziyal to the opening of her exhibit. Kira points out that "He's a self-righteous sycophant who despises everything Bajoran," and notes that Damar sneers whenever he says "Bajoran". Dukat denies this just as Damar walks in, giving a report and sneering whenever Bajorans are mentioned. Kira can't help but laugh. Damar glares at Kira, but continues his report and leaves. Dukat then imitates Damar, causing Dukat and Kira to laugh together. The script for this episode, including the deleted scene, can be viewed here. The scene also appears in the novelization of this episode.
- Ron Moore commented, "You may argue that we should've cut more from the Worf/Alexander story, but if you look at the show objectively you'll see that there's not a lot of extra material in that story to chop." (AOL chat, 1997)
- The opening scene as shot for this episode was different from the opening scene that aired, but it had to be cut for timing reasons. Originally, the episode opens in Kira's quarters, with Kira and Jadzia Dax looking at Ziyal's paintings. Dax points out that Kira still misses Ziyal, to which Kira answers, "I'll get over it. Death and I are old friends." Dax then suggests that Kira bring Death to dinner. They get up and leave the room, and the scene then picks up in the corridor as seen in the finished episode. (Star Trek: Deep Space Nine Companion)
- A scene was shot in which we see Sarina untie Julian Bashir, and actually speak to him, but the scene was cut for time. 
- A scene cut from the episode saw Sisko, Worf, Garak, and O'Brien selecting a Cardassian target to attack. The Torg'Q system was the first to be suggested by Worf, as it was the closest system along the border to Cardassia Prime, however it was also the most heavily fortified. One advantage of this fact was that the Dominion would never expect an attack there, but the disadvantage was that the element of surprise might not last long, resulting in heavy casualties. The Ventani system was the second target, chosen by Garak, because Ventani II was the birthplace of Tret Akleen, the father of the Cardassian Empire. Garak suggested that such a loss of sacred ground would be devastating to the Cardassians, and a great propaganda victory. Disadvantages of this target were that the system had little strategic value, and its loss would have no effect on the Jem'Hadar. O'Brien finally chose the Chin'toka system, because he had noticed that sensor scans of the warp signatures from the Dominion fleet stationed there was slightly different (and almost "too synchronized") than previous scans, suggesting that they were fake signatures. 
- A deleted scene in this episode involved Quark sitting at the bar and lamenting his failure with Ezri, and Jake attempting to cheer him up by making him a drink. The scene would have gone between the scene where Quark hears Ezri talking about Kor and thinks she is talking about Worf, and the scene where he confronts her about her feelings. In the scene, as Quark pours out his heart to Jake, Jake is getting flustered because he is trying to concentrate on making the drink, but Quark keeps distracting him, and he keeps getting it wrong, pouring it out and having to start again. The scene was cut for time. (AOL chat, 1998)
- Two scenes were shot for this episode which didn't make it into the final cut, but can be found in the script:
- In a deleted scene for this episode, Kira Nerys, Damar, and Garak get drunk in Enabran Tain's basement. The tail end of the sequence is still in the episode, seen when Kira is lying down playing with an empty bottle. (citation needed • edit)
- Ronald D. Moore revealed that in a deleted scene,cut for time, "Ezri asked Worf what it was like to stand at the pinnacle of the Empire for a moment and Worf said he remembered wishing his father had been there to see it."  The script of that deleted scene can be retrieved at the Italian Trek database HyperTrek. 
Star Trek: Voyager
- A scene cut from this episode's teaser features Janeway participating in a Gothic-era holonovel. (A Vision of the Future - Star Trek: Voyager, pp. 10-12, 18-20, et al.) The same scene was ultimately included in the teaser of "Cathexis", with minor differences from "Eye of the Needle"'s shooting script.
- In a scene deleted from this episode, Harry Kim practices clarinet in his quarters but, to Tom Paris, he bemoans the area's lack of soundproofing. The scene was to begin the episode and was filmed on the first day of the episode's production, before being cut. Despite being removed from "Death Wish", the scene was later incorporated into "The Thaw".
- A scene cut from this episode was to have addressed the break-up of the relationship between Neelix and Kes (which occurs in "Warlord"). The scene was cut for time. (Star Trek: Voyager Companion, p. 159)
- A scene deleted from this episode features the Delaney sisters at a champagne reception, wearing the teal blue sciences uniform. A still from this scene was used for early publicity for the episode.
- In a deleted scene, a female member of Kelis' species who portrayed a Klingon acted in the ancient Greek theater. (This character was played by actress Carissa Hernandez and her dialogue and scenes were removed from the episode.)
Star Trek: Enterprise
- Three deleted scenes were made available on the DVD for the episode "Broken Bow". The details of these scenes can be viewed in the episode summary.
- Two deleted scenes were made available on the DVD for the episode "Fight or Flight". The details of these scenes can be viewed in the episode summary.
- One deleted scene was made available on the DVD for the episode "Unexpected". The details of this scene can be viewed in the episode summary.
- One deleted scene was made available on the DVD for the episode "Sleeping Dogs". The details of this scene can be viewed in the episode summary.
- Scene 2 of this episode was cut from the final aired episode. In this scene, the Risian Freebus, played by Dennis Cockrum, talked to Archer, T'Pol and Tucker in the mess hall and received his payment, dilithium, for the shore leave of the crewmembers. Also in this scene are background performers Dawn Drake and Glen Hambly. The scene was later included in the ENT Season 1 DVD.
- Scene 41-42 were cut due to the length of the episode. They included the Chinatown scenes and guest performers Serena Scott Thomas (Becky) and Jim Lau (maitre d') as well as sixteen background performers and Scott Bakula. The scenes were later included in the ENT Season 2 DVD.
- Scene 44 was also cut. The scene involved Linda Park and Scott Bakula and was later included in the ENT Season 2 DVD.
- A scene with an aged Porthos (twelve years older) was shot for the future sequences, but didn't make it into the final show. In the "present" scenes, a scene was cut at movie night where Archer told T'Pol about Porthos being stressed - and that he might benefit from neuropressure.
- In a scene, deleted from the final version, one of the Sphere Builders was electrocuted when she tried to damage the ships systems. (Source: Alina Andrei)
Star Trek films
- Approximately twelve minutes of scenes were cut from the theatrical cut and later reinstated for the film's 1980 video release as the "Special Longer Version". This version also aired on ABC in 1983 and can also be seen on Side 2 of the Director's Edition DVD. These deleted scenes include: a scene where Sulu is stumbling while showing Lt. Ilia the navigator's console, and a scene where Kirk is departing the Enterprise after Spock begins his quest into V'Ger. The scene is notable for being unfinished, resulting in the sound stage walls and ceiling being seen in the scene. Another deleted scene includes a space walk sequence in which Kirk and Spock explore V'Ger. The scene failed in screen tests and was never completed. (Star Trek: The Motion Picture (The Director's Edition) Special Features)
- Many scenes involving the character of Peter Preston, including those which reveal him to be the nephew of Montgomery Scott. Some of these scenes were re-added for the director's edition. Another scene, where Kirk tells Spock that David Marcus is his son, was cut, but restored for the director's edition. Another scene (a conversation between Kirk and Spock after the Kobayashi Maru test) established that Saavik was half-Romulan. 
- A scene which was originally filmed to give the character Hikaru Sulu a look at his great-grandfather whom he met as a young boy while in a backstreet of San Francisco was excluded from the final movie. The boy who was cast to portray Sulu's ancestor was so unsettled by his mother, who was also on set that day, that producer Harve Bennett decided to cut this scene because of the unacceptable acting ability of the boy. (Trekworld, June 1999)
- A scene in which Colonel West proposes Operation Retrieve to the Federation President and a later scene in which the Klingon assassin is revealed to be West in disguise. They were restored for the VHS and DVD releases of the film.
- A scene in which Spock, Valeris, and Scotty discuss the whereabouts of Kirk and McCoy, (and Scotty claims, referring to Azetbur: "I'll bet that Klingon bitch killed her father!") was also cut from the theatrical release, but was restored for the VHS and DVD releases.
- An alternate take of the Enterprise's communication with the Excelsior where Sulu begins by saying "This is Captain Sulu, USS Excelsior."
- An extension of the Enterprise's approach to Khitomer where Kirk orders all hands to battle stations. (citation needed • edit)
In addition to the alternate opening, there are many cuts to the movie, including:
- A scene after Harriman, Montgomery Scott, and Chekov discover that deflector control has been destroyed aboard the Enterprise-B where Ensign Sulu tries to use the ship's sensors to locate Kirk and Chekov laments that he never thought Kirk's life would end the way it appears to. Scotty reminds Chekov that "all things end, laddie" while Harriman orders the ship home.
- A short trim on the holodeck scene where Dr. Crusher asks Geordi La Forge if the holodeck safety protocols are on-line just before Worf attempts to jump for the hat.
- An alternate take of Data pushing Beverly Crusher into the water, where Worf shoots Riker a dirty look after climbing back aboard and Dr. Crusher refuses Data's help.
- A short trim on the Ten Forward scene where after asking for more of the disgusting drink from Frocas III, Data takes another sip and is again revolted, effectively ruining the joke.
- An alternate take of Data's emotional seizure aboard the Amargosa observatory where he experiences many more emotions, including one with an obvious sexual overtone.
- A scene after Dr. Soran orders the Klingon ship to the Veridian system where a Klingon officer brings La Forge's unconscious body to the bridge where Dr. Soran has him brought with him for interrogation. The scene then shifts to the USS Enterprise-D where Worf and Riker discover that the Bird-of-Prey belongs to Lursa and B'Etor and find Data being examined in sick-bay by Dr. Crusher who tells them that the emotion chip has been fused into his neural net and cannot be removed. Data expresses concern for La Forge's safety while Dr. Crusher briefs Riker and Worf on Dr. Soran. This scene was later referenced by Captain Picard in a log entry in the final cut.
- The "La Forge Torture" scene where Dr. Soran uses a Borg nanoprobe to stop La Forge's heart, causing him agony. Soran interrogates La Forge for information on how much the Enterprise-D crew have figured out of his plans and if Guinan has told the crew about him. On the DVD commentary, it is stated that Soran's line about La Forge's "heart just wasn't in it" is a reference to this scene. Later, Dr. Crusher mentions that she removed the nanoprobe.
- A short scene where Lursa and B'Etor spy on La Forge taking a bath. This scene was referenced later in the final cut where B'Etor complains that La Forge is the only Starfleet engineer who doesn't go to engineering.
- A short scene where Dr. Crusher leads her patients and staff out of sickbay in preparation for the saucer separation.
- Various shots of Dr. Crusher and La Forge leading their parties to safe locations while crewmembers remove all breakables from high altitudes in preparation for the crash.
- An alternate take of the crash sequence where Picard's family album is knocked off his desk in the ready room as the crash begins. As the ship skids along the surface of the planet, Worf breaks open the equipment locker on the bridge and tosses Data a palm beacon as he tries to protect Counselor Troi at the helm. Meanwhile, Worf props another injured crewmember into Riker's chair.
- An alternate take of the Picard family Christmas where the children present him with a sextant (which Thomas Picard refers to as a "sack-tent.")
- An alternate take of Picard convincing Kirk to join him on Veridian III where Kirk compares the Nexus to orbital skydiving; exciting at first, but, ultimately empty. Kirk also realizes that Spock's advice of taking on such a mission would be illogical is correct.
- An alternate climax where Kirk takes many of the falls that Dr. Soran takes in the final cut. After Kirk retrieves the PADD, he quips "The 24th century isn't so tough" just before Dr. Soran shoots him in the back with a hidden phaser in his boot. As he dies, Picard sets the solar probe to explode too early, foiling Soran's plans. Soran rushes Picard, who grabs Soran's phaser and kills him, while Kirk dies without saying a word.
- A scene where La Forge and Worf rescue Picard in the shuttlecraft Hawking. Picard notices the damage to the shuttle and asks if the Klingons had given them any trouble, to which La Forge replies "You could say that."
- A scene where Dr. Crusher and Nurse Ogawa sort through the shattered remains of the sickbay where Crusher wonders if she should take a stretcher herself, due to the exhaustion of treating so many patients. (citation needed • edit)
- A short scene cut from the film happened on the holodeck, when a drunk named Buster grabbed for Lily Sloane's arm and was pushed back. 
- In another scene, Zefram Cochrane – reluctant to make the first flight of the prototype warp ship Phoenix – was chased by officers from the USS Enterprise-E and became trapped at the edge of a cliff. As he was about to jump to his death (thereby committing suicide), Troi had to climb onto the cliff and try to persuade him to come back down. She eventually told him to jump, though, and even pushed him off the ledge. His descent was not fatal, however, as his fall was stopped in mid-air by a force field that Geordi La Forge had rigged up. Explained co-writer Brannon Braga, "That just got cut for time. We felt we had enough Cochrane character bits, so we just cut that out." (Star Trek Monthly issue 26, p. 35) "I was sorry they took that [scene] out," said actor James Cromwell, who performed the scene at his audition for the role of Zefram Cochrane, "but we discussed it and it didn't make sense." Cromwell believed that, if Cochrane was suicidal, he would have had no problem with agreeing to make the initial warp flight, though his reluctance to do so (and him overcoming this hesitancy) is one of the film's main story points. (Star Trek: Communicator issue 111, p. 71)
- Both the teaser and theatrical trailers included footage unique only to them, with some visual effects created specifically for the trailer. Unique shots included the USS Voyager firing phasers at a differently-designed Borg cube and an alternate version of Picard's soon-to-be infamous speech, "The line must be drawn here!" in the teaser, and cut takes of various Borg drones in the theatrical. In the UK theatrical version of the film there were two scenes that were cut from subsequent VHS and DVD releases; One taking place after Worf is transported over to the Enterprise-E, where he refuses medical treatment from Dr. Crusher and demands to be taken to the bridge, and an extended scene on Earth where Zefram Cochrane asks Geordi La Forge about his eyes. This appears to be the only evidence of cut material; no deleted scenes have surfaced or been officially released. 
- Ru'afo's Face lift (Scene #32): Includes a few extra seconds of footage of the skin-stretching procedure during Ru'afo's first conversation with Admiral Dougherty.
- Working Lunch (Scene #36): Captain Picard spills his salad on his uniform while doing research on the Briar Patch in his quarters. Commander Riker enters and they discuss the features of the region.
- Flirting (Scene #40): Extended footage of Riker and Troi's research on the Son'a in the ship's library. The two officers banter back and forth and throw scraps of paper at each other like schoolchildren while being shushed by a stern librarian. Max Grodénchik appears in the scene as a Trill Ensign though he has no lines. The relevant plot points from this scene were included in the theatrical version.
- The Kiss (Scene #155): Anij and Picard's kiss, filmed in super-slow motion, as the Ba'ku have the ability to slow down time. Co-Producer Lauritson comments that "although it read well on paper, it just didn't work when we cut it together. So we just dropped that part of it."
- Status: Precarious (Scene #268): After his attack on the Son'a ship, Data beams himself out of the Cousteau immediately before it explodes.
- Disabling the Injector (Scene #270-277): Additional dialog between Picard, Riker, and Worf immediately before Picard beams aboard the metaphasic collector.
- Alternate Ending (Scene #301-304): Alternate death scene for Ru'afo. He is rapidly de-aged by the metaphasic radiation of the Ba'ku rings, using a series of younger and younger actors. Lauritson explains that Paramount Pictures felt the original ending was too "soft."
- A further deleted scene featured Armin Shimerman as Quark, who arrives on Ba'ku aboard the USS Ticonderoga to open up the planet as a vacation spot; he is dismissed by Picard and escorted back to DS9 by an irritated Worf. This scene was scripted and filmed but not included on the Special Edition DVD, although a still picture from it can be seen among the special features.
Seven deleted scenes appear on the DVD edition with introduction by producer Rick Berman. In the intro, Rick Berman confirms that roughly fifty minutes of footage was trimmed from the original version. The seven deleted scenes make up about seventeen minutes of this original footage and include:
- A private conversation between Picard and Data over a glass of wine.
- Early introduction of Shinzon in the film (right after the wedding reception). This is the scene that includes the dialog from the theatrical trailers, "But in darkness there is strength..." (Viceroy) and "The time we have dreamed of is at hand... the mighty Federation will fall before us..." (Shinzon).
- The second mind-rape scene of Counselor Troi in a turbolift.
- A scene of Picard walking with Troi down a corridor and Troi explaining to him that he and Shinzon are two different people. This scene includes the line from the trailer, "it was like a part of me had been stolen..." (Picard).
- Sickbay getting ready for battle, a short dialog between Dr. Crusher and Picard is shown.
- Worf warning Picard about the Romulans just before they leave for Romulus. This scene includes the dialog from the trailer, "I recommend extreme caution..." (Worf).
- The original extended ending - a new First Officer is introduced on board the Enterprise and two funny moments are shown afterward. Instead of ending while the Enterprise is docked above Earth, this alternative ending shows the Enterprise warping away.
- A conversation at the wedding between Picard and Wesley Crusher, who explains that he will be serving as an engineer aboard the USS Titan under Captain Riker.
- A scene in the Enterprise mess hall in which Riker, Troi, and Worf discuss the differences between human and Klingon honeymoon traditions, and Data attempts to share a meal with B4.
- A scene of La Forge and Worf clearing out Data's personal effects from his quarters, in which several props from the TNG series (including Data's violin and the pipe he smoked as Sherlock Holmes) appear. Spot the cat also appears jumping into Worf's arms; when Worf states that he is "not a cat person," La Forge responds "Looks like you are now!"
- A scene which shows Amanda holding newborn baby Spock on Vulcan with Sarek. This scene appears in several trailers. In the audio commentary, Abrams explains that this was to be the very first scene in the film, preceding the USS Kelvin scenes, and that it was cut because it was felt that there would be too much back-and-forth in combination with all the other young Kirk and young Spock scenes.
- A scene where young Kirk witnesses an argument between his brother George and their uncle Frank, prior to Jim's decision to steal the Corvette.
- An extension of the scene with Sarek and young Spock where Sarek and Amanda argue over young Spock's fight with the bullies at the Vulcan school.
- A scene which shows Nero as a prisoner on the prison planet, which turned out to be Rura Penthe. It was Nero's escape from Rura Penthe which Uhura heard about in the transmission she received regarding an attack on a Klingon prison planet. These scenes feature many actors and stunt performers as Klingons and several background aliens from the prison planet such as a multi-eyed alien.  This sequence also contains Nero's line, "The wait is over", as seen in trailers for the film.
- A longer version of Kirk's conversation with Gaila and the subsequent Kobayashi Maru scenario, in which it is revealed that Kirk took advantage of Gaila's feelings for him to reprogram the simulation (via a message from him to her, which she received during his test) - the production staff's DVD commentary would explicitly describe Gaila's visibly annoyed appearance during Kirk's subsequent hearing as a holdover from this scene.
- A scene on board the Enterprise in which Kirk attempts to apologize to Gaila, but mistakes another green-skinned female for her.
- A brief shot in which Spock Prime walks near Sarek, who seems to sense his presence.
- Several other aliens were created for the film, including Barney Burman's homage to the M-113 creature, a salt sucker. 
- Kirk recording his captain's log, falsifying the events on Nibiru.
- A scene shows John Harrison having a shower in the brig.
- Alexander Marcus watching news reports in his office.
- Carol Marcus mentions to Kirk she was raised by her mother in England.
- An extended dialogue scene between Carol and her father. 
- Kirk meeting Rima and Lucille Harewood at the memorial at the film's conclusion.