Star Trek Into Darkness is the twelfth film in the Star Trek film series, released in 2013.The sequel to 2009's Star Trek, it is the second film to be directed by J. J. Abrams. Along with returning actors from the previous movie such as Chris Pine as Captain Kirk and Zachary Quinto as Mr. Spock, the film features an All-Star Cast by bringing Benedict Cumberbatch, Alice Eve and Peter Weller on board. Noel Clarke also makes a brief appearance.Tensions are high upon the USS Enterprise as Captain James T. Kirk and his first officer Mr. Spock clash over their conflicting philosophies regarding professional and personal honor after a mission in which Kirk violates the Prime Directive. But when a rogue Starfleet agent, John Harrison, embarks on a campaign of terror against the organization, the crew of the Enterprise is assigned the duty of traveling to the volatile Klingon homeworld and bringing him to justice. Of course, all is not as it seems: there might just be a Bigger Bad lurking behind the rogue officer, and Harrison may be more than he claims to be...The film was a commercial success—the highest-grossing in Star Trek history—and was well-received by critics. As per usual, however, a Broken Base developed around its tone, the use of a Race Lift, and its plot, which references events in the Prime continuity in a way that some disagreed with.Watch the announcement teaser here and the full trailer here.
This movie provides examples of:
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2-D Space: In Star Trek II: The Wrath of Khan, Khan's lack of experience in space battles make him vulnerable to attacks on the Z-axis (above and below). The USS Vengeance is designed by Harrison with a bridge that, due to the cutout in the saucer section, is vulnerable to attack from above and below.
Abandon Ship: Spock orders the Enterprise abandoned when she is crippled and falling from orbit over Earth. The ship's tumbling badly hinders the evacuation, as crew members are sent falling to their deaths via Gravity Screw and a brief view of the shuttle bay shows the escape shuttles are similarly being tossed around. The ship is saved and the evacuation averted in the end.
Several others as well, Uhura and Spock's conversation on the shuttle to Kronos (though this gets interrupted), and Kirk's conversation with Harrison/Khan on the ship.
Action Prologue/Batman Cold Open: The opening sequence set on Nibiru shows the Enterprise on an action packed away mission that will have nothing to do with Khan or the main plot.
Adaptational Badass: The original Khan that Ricardo Montalban portrayed is nothing to scoff at, thanks to his charisma and dangerous intelligence. But here, in addition to those traits, Khan is also shown to be much more physically powerful, going straight into One-Man Army levels.
Adaptational Villainy: The film gives a darker view on Khan's origins. In the original series, Khan's origins depicted him as a "benevolent tyrant" who was repressive but not wholly murderous. Into Darkness has Spock state that history indicates that Khan and his followers were planning to destroy those deemed inferior. Khan doesn't confirm it but doesn't deny it either. The tie-in comics show that Khan genuinely saw himself as humanity's savior and that he explicitly wanted to rule, not destroy. However, the methods he employed to achieve his goal (including nuking Washington D.C. and Moscow) would certainly justify humanity recording in their history that he was an Omnicidal Maniac.
The death of Pike. He knew he was dying, was in considerable pain and was terrified. Despite Spock's effects to comfort him, he died that way.
Kirk's death. Imagine being in Spock's place, having to watch his best friend die of radiation poisoning while being completely helpless to do anything to save or comfort the former. To makes things worse, Spock experienced this helplessness twice, once with Pike and now with Kirk.
Even with the medical advances of the 23rd Century, Thomas Harewood(Noel Clarke) was watching his daughter die. John Harrison took advantage of Thomas' desperation to get him to suicide-bomb the Starfleet records office in exchange for a cure for his daughter's disease.
The Prime Directive (which is the codifier for this trope), the set of rules stating Starfleet personnel avoid interfering with less developed alien cultures, is discussed during the opening away mission. In this case, Kirk gets demoted and temporarily loses command of the Enterprise for violating it. It's worth noting that unlike other cases were the Prime Directive is used to justify letting an alien species die, Pike is more angry that Kirk got into a situation in the first place were he either had to obey the Directive or save a crew member.
The Temporal Prime Directive is alluded to by Spock Prime, who's vowed to never reveal information about the future as it happened in the Prime Reality, unless it's absolutely necessary.
All There in the Manual: The novelization fills in a major plot hole. After the Tribble comes back to life, McCoy discusses with Carol Marcus why he can only use Khan's blood to revive Kirk, and not one of the 72 other augments in stasis.
All Your Base Are Belong to Us: John Harrison targets a Starfleet data storage facility in London that turns out to be a facility for Section 31, the Federation's black operations group, and tries to destroy Starfleet Headquarters in San Francisco.
Harrison: Have I got your attention now?
An Aesop: Listen to your friends and advisers. In order of occurrence;
If Kirk had listened to Spock and not lied in his report, he would have been able to defend his actions at the inquest instead of being chewed out by Pike, which at the very least would have delayed his demotion long enough for him to still be a captain when Khan attacked.
If Pike hadn't pulled a Not Now, Kiddo on Kirk at the captain's meeting he would have figured out Khan's plan a few precious seconds earlier, possibly saving the lives of all present.
If Kirk had listened to Scotty's complaints and let him check the payload of the torpedoes, instead of overruling Scotty so he could pursue his vendetta against Harrison, the frozen super soldiers would have been discovered, undoing everyone's plans.
Had Kirk not listened to Spock and killed Harrison with the torpedoes, he would have aided Marcus' plan to start a war. Granted, it did end up getting him killed and San Francisco leveled by a starship, but those things might have happened anyway if a war started.
More importantly, don't let your desire for revenge compromise you, lest you pay the price for it. And good friends and advisers will point this out to you.
Anachronism Stew: In the midst of Space Brasilia, a San Francisco tram can be seen trundling along in the background, presumably kept for nostalgia/tourist reasons as in contemporary cities.
Ancient Astronauts: From the point of view of the species that the Enterprise saves in the beginning.
And the Adventure Continues: Or rather, the adventure begins, with the film ending as the Enterprise leaves Earth to begin its five-year deep space exploration mission, which was the basis for the original series.
Also, with the threat of a Klingon/Federation war on the horizon. The tie-in comics confirm that the Klingons are planning to declare war on the Federation after obtaining photographic evidence of Kirk being on Qo'noS.
Apathetic Citizens: A giant spacecraft has just crashed into San Fransisco. People notice, but as Spock pursues a fugitive through the city most folks are just going about their business as if this sort of thing happens every day.
Also, the Enterprise exits warp with Earth partially obscured by the Moon and from then until it enters the Earth's gravity well is a huge ball of problems regarding distance, time and the various forces involved - either inertia carried them to Earth (in which case they spent too long near the Moon) or they had limited inertia and should not have been able to reach Earth in that short of a timeframe. Liberal helpings of Rule of Drama required. Also notable is informing the distance to Earth in several thousand kilometers... but the actual number could only have been less than fifty kilometers at the most.
In the opening scene, Spock uses a "cold fusion" device to freeze the volcano. However, the term "cold fusion" is used to describe a hypothetical fusion reaction that doesn't require extreme heat to occur — not one that generates extreme cold.
Even though it's Lampshaded by Scotty, it is a really bad idea to put a spaceship underwater. Yes, it's airtight... but a spaceship is designed to resist being pulled apart from internal pressure, and a submarine is designed to resist being crushed from external pressure. When it comes to your Cool Starship, it can stand anywhere between zero and one atmospheres of pressure. The Enterprise isn't even in all that deep (probably just enough that it can't be seen from the surface), yet it's still noted to be leaking in places.
Artistic License - Ships: A terminology example, though it leaves some questions about the engineering as well. Harrison identifies the Enterprise's life support system as being located behind the aft nacelle. "Aft" meaning "rear", this could refer to either nacelle. Furthermore, there is nothing behind the nacelles. They're the furthest aft things on the ship. It wouldn't make much technical sense to have primary life support control installed on them either; people aren't meant to bunk up there.
As You Know: The opening scene is filled with it. Sulu has to tell his co-pilot that the shuttle wasn't designed for the heat of a volcano, Spock has to tell everyone that the volcano will destroy the planet, Uhura has to tell Spock that he might die, Sulu has to tell Spock that the shuttle wasn't designed for this amount of heat, Spock has to tell everyone that his device will detonate when the timer reaches zero, and Sulu and Scotty have to tell Kirk that the ship won't withstand the heat. They all knew what they were doing and what the mission was.
Attack Drone: The Vengeance could launch drones that in turn were capable of launching several photon torpedoes before crashing into a target.
Author Tract: Producer and co-writer Roberto Orci is a 9/11 truther, and the basic plot (false-flagging a terrorist attack for the explicit purpose of starting a war) is straight from those theories. By pure coincidence, the connection is hammered home with a tribute to 9/11 veterans in the credits, which was actually put in because a lot of the extras were veterans.
Harrison calmly boasts multiple times about his superhuman abilities.
John Harrison: I am better. Kirk: At what? Harrison:Everything.
Kirk makes an offhand boast while escaping with Spock and Uhura from a pursuing Klingon interceptor.
Spock: This ship has no offensive capabilities. Kirk:It's got us; give me all six fuel cells.
Lampshaded with Acting Captain Sulu's warning to Harrison:
Sulu: Attention: John Harrison. This is Captain Hikaru Sulu of the USS Enterprise. A shuttle of highly trained officers is on its way to your location. If you do not surrender to them immediately, I will unleash the entire payload of advanced long-range torpedoes currently locked on to your location. You have two minutes to confirm your compliance. Refusal to do so will result in your obliteration. And if you test me, you will fail. Bones:[beat] Mr Sulu, remind me never to piss you off.
Badass Longcoat: Harrison likes wearing futuristic trenchcoats. Near the end of the film, he even steals a replacement someone had conveniently left on a chair. Presumably, this was to help disguise him to some extent.
Some of the Klingon patrols on Qo'nos sport these.
Bat Deduction: Kirk figures out that the archive bombing was a ruse to gather Starfleet's command into the briefing room. While he's correct, it's his first guess, which comes off as a rather abrupt leap of logic.
Batman Gambit: The suicide bombing that Harrison orchestrates early on is a ploy to get Starfleet's highest ranking officers to follow Federation protocol and hold an emergency meeting, whereupon he attacks the meeting room.
Likewise Marcus counted on Kirk being a rule-breaking maverick who was also enraged at the loss of Pike to fire the torpedoes at Q'onos to eliminate Khan and start the war Marcus wanted while pinning the blame on Kirk since the mission was off the books. He just didn't expect Kirk to be a Spanner in the Works.
Khan's entire plan was a Gambit Pileup, as he also relied on Marcus to send exactly those 72 torpedoes after him which he himself had loaded with his own crew members in cryosleep.
Battle Couple: Spock and Uhura when they're fighting Klingons on the war-world of Qo'noS, and when Spock battles Harrison in the climax, Uhura quickly beams in to help.
Beam Spam: USS Vengeance, which fires down an extreme salvo that totals the Enterprise within minutes. Remarkably, averted for the Enterprise; she doesn't get to fire a shot before the weapons systems are taken out.
Beauty Is Never Tarnished: Carol Marcus gets fed a piece of the scenery by Khan when she gets in his way, and shortly afterwards has her leg stepped on by him, complete with sickening crunch. Cut to a shot of her being dragged to a teleporter and sickbay, and she has absolutely no external signs of injury. However, before she gets brought in to sickbay, when they are initially sent back via Khan off the Vengeance- into a holding cell on the Enterprise, look closely and she does have a noticeably large black and blue swollen area encompassing most of what appears to be her knee area- granted the trope is still mostly in effect as the damage is rarely seen after that and of course, her face is perfectly fine.
A male example: When Spock was dying of radiation poisoning in Wrath of Khan, he had burns on his hands and face. In this movie, Kirk doesn't get any of that.
Spock when Kirk dies from radiation poisoning from having to enter the energy core to manually fix the Enterprise after Khan shot it. Beating Khan to death, considering Spock was all originally for a fair trial for Khan, until Uhura tells him to stop is some serious berserk button issues.
Unless you wish to face the wrath of Lieutenant Uhura, do not hurt Spock. You have been warned.
Also, lest you wish to face the wrath of the Klingons and Lieutenant Uhura, do not interrupt Uhura while she's negotiating with the Klingons.
Threatening Khan's crew or implying that they're dead is a seriously bad idea. Admiral Marcus found that one out the hard way.
Best Served Cold: Spock assumes that Harrison's ultimate plan is to finish what he had started: Kill anyone he considers "inferior." Harrison doesn't deny this. (This is appropriate, of course; Harrison is actually Khan Noonien Singh, the Trope Namer.)
Big Bad: John Harrison, a Starfleet agent with superhuman abilities turned terrorist. He's really Khan Noonien Singh, an infamous war criminal working for Starfleet under an assumed identity.
Big Bad Ensemble: Khan and Admiral Marcus. The former wants to revive his crew of superhumans and take over the Earth, while the latter plans to sacrifice the Enterprise so he can start a war with the Klingons. Two thirds of the way through the movie, Khan betrays and kills Marcus.
Big Bad Wannabe: While Marcus is a credible threat and even manages to kick the shit out of the Enterprise, he becomes nothing more than a tiny little blip on a radar the moment Khan gets his hands on him.
Bling of War: Averted. Starfleet's dress uniforms are simple and utilitarian; even their rank insignia has a matte finish. The closest they get to bling are the black uniforms and sky blue sashes of the honor guard.
Bloodless Carnage: Harrison's hands and clothes are surprisingly clean for someone who just popped a man's head like a tomato.
Blunt Yes: Scotty threatens to resign over the presence of the experimental photon torpedoes on the Enterprise, saying he won't sign for anything if he doesn't know how it works. Kirk accepts.
Book Ends: The film's intro and climax feature a Federation starship rising from and crashing into the sea, respectively.
Break the Cutie: Carol Marcus finds out her father is a backstabbing warmonger, gets betrayed by Harrison/Khan, gets her leg snapped in half, and then watches as Harrison crushes her father's head with his bare hands.
Broken Faceplate: Realistically played straight. During the space jump, Kirk takes a winging glance to the face from a small piece of debris. It produces a hairline fracture on his faceplate which begins to expand into a spiderweb of cracks as the air pressure in his suit push the faceplate outward. It holds and does not shatter completely, but it does disable his Heads-Up Display.
Brick Joke: Of a very dark variety. During Harrison's Hannibal Lecture to Kirk and Spock, he says that Spock can't even break a rule, so how can he be expected to break bone? Fast-forward to Spock's berserk rage after Kirk dies, and what does he do? Break Harrison's arm at the shoulder, complete with Sickening Crunch.
Bullying a Dragon: Kirk should have known better than to smack Harrison around like that, especially after he surrendered. Marcus's overall treatment of Harrison also falls into this category.
The transwarp beaming tech provided by Spock Prime is instrumental in Khan's attack. Similarly, aside from the scientists studying it, the only person who knows how to use it is Scotty, who created it in the Prime timeline.
Spock goes to Spock Prime for information on Khan.
Kirk talks with Pike about the scene in the previous film where Pike asked Kirk to join Starfleet.
At one point, several models of ships (showing off Humanity's progress towards space travel) are panned across. In that lineup are the Phoenix and an NX-class starship.
Another McCoy moment is when he asks if Carol gets airsick after she'd been beamed onto Enterprise and getting treated for her injuries. This is of course a callback to him freaking out right before taking a shuttle in the previous film and how he'll might puke on Kirk during their trip up to the Enterprise.
Scotty resigns before the mission after vehemently disagreeing with Kirk on using unidentified Photon Torpedoes. Kirk later enlists his aid in investigating Harrison's claims, culminating in Scotty sneaking on board the Vengeance and disabling it to save the Enterprise.
Pavel Chekov, who is not the Trope Namer for Chekhov's gun but is in fact named after him, manages a surprise save of Kirk and Scotty. Yep, he was still down in Engineering.
Admiral Marcus and Section 31, who betray both the Enterprise and their own ruthless superhuman agent to try and start a war with the Klingons.
Khan, too. The Enterprise was incapable of threatening him, he had the most powerful ship in Starfleet, and theoretically his crew returned. He doesn't even bother to check on that last bit before deciding to blow up the Enterprise, even though he'd have been untrackable if he'd simply left.
Cloak & Dagger: Section 31, the Federation's clandestine black-ops group, meant to destroy any threats to the Federation at any cost - including breaking the Federation's own tenets.
Colour-Coded for Your Convenience: This film plays Dark Is Evil very straight with Harrison's all-black clothing and the Vengeance, but when Kirk and Harrison prepare to space jump, it goes the extra mile by making the collar of Kirk's suit a subdued gold, and the collar of Harrison's... black.
It seems that the standard Starfleet gear for anyone who doesn't have a role on the ship comes in black: Kirk's uniform during most of the first movie had black accents, as he wasn't actually part of the crew.
Commissar Cap: This seems to be part of the Star Fleet dress uniform. They are particularly visible in the gathering at the end of the film.
Conservation of Ninjutsu: Several squads of Klingons vs. four main characters. Three guesses who wins and the first two don't count.
Although the five year mission doesn't begin until the end of the film, the official IDW comic book series has established that by this point the Enterprise crew has experienced a number of the adventures and missions that, in the original timeline, took place during the five-year mission. Hence, the existence of a Tribble on the Enterprise now, rather than the doctor first encountering them later on.
Also, the ship Kirk uses for a clandestine landing on Kronos was captured during "the Mudd incident".
McCoy performs surgery on a photon torpedo with a science officer, again. This doubles as a Stealth Pun, a Stealth Visual Pun, or even a Shout-Out to the original Chris Rock act since the good doctor spends a great deal of his screen time performing 'Rocket Surgery'.
Admiral Pike's line "They gave her back to me. The Enterprise." is the same line (then) Admiral Kirk says to Scotty in Star Trek: The Motion Picture before boarding the Enterprise.
A building known as "The Kelvin Memorial" can be seen in the background of one scene, referencing Kirk's father's doomed ship from the first movie.
The ship used by the Enterprise crew to infiltrate Qo'noS was confiscated weeks before from someone named Mudd. Note: In a case of All There in the Manual, this is a not actually Harry Mudd, the conman from the original series. It is a reference to an event in the IDW comics prequel in which a female smuggler named Mudd (implied to possibly be the daughter of Harry) encountered the Enterprise crew.
Khan and his crew being 300 years old, and responsible for a eugenics plot against the world. Its a call back to Khan's backstory in "Space Seed".
Admiral Marcus has the Phoenix, the NX-01 as well as a XCV-330 among his office collection of models depicting forms of Earth flight and space travel from the Wright brothers' first plane through a V-2 rocket, Vostok, and Gemini.
Also from Star Trek: Enterprise: the offshore stadium in San Francisco is still there, visible in at least one aerial shot of the city.
Also, Carol telling her father that she's ashamed to be his daughter is the opposite of her son David telling Kirk that he's proud to be his son in The Wrath of Kahn.
The Enterprise takes a massive beating by another Starfleet vessel, the USS Vengeance, leading to serious damage to the engineering section, just like how the Enterprise took a beating by the USS Reliant.
Looking at the Vengeance from the side (especially when it first meets the Enterprise), shows it bears a striking resemblance to the USS Enterprise-D from Star Trek The Next Generation, with a nacelle design similar to the USS Enterprise-E from the Next Generation movies.
Kirk incapacitates Scotty before going to repair the warp core, just like how Spock incapacitated McCoy under similar circumstances.
Kirk still likes the Beastie Boys, listening to "Body Movin'" during sex, referencing him listening to "Sabotage" as a kid in Star Trek.
Sulu takes the conn and has to act as temporary Captain, alluding to him becoming captain of the Excelsiorin the original continuity. He also has to bluff to Harrison; Chekov did something similar in Star Trek V.
Scotty manages to swiftly sabotage a really high-tech Starfleet prototype. Sound familiar?
Harrison notes "No ship should go down without her captain", a line from Moby-Dick, a novel which Khan Noonien Singh loved.
At one point, Harrison threatens to incapacitate the Enterprise crew by depriving them of oxygen. Khan took over the Enterprise using this method in the TOS episode "Space Seed".
Despite surviving a nerve pinch, phaser shots, and a lot of beating, Khan eventually goes down after Spock hits him with a piece of metal. Kirk likewise incapacitated him with an engineering tool in "Space Seed".
Also, Uhura speaking Klingon may be a Take That to the translator scene from Star Trek VI: The Undiscovered Country. Nichelle Nichols was unhappy that her character, a veteran communications officer, would not speak fluent Klingon. Perhaps as a nod to the original scene, Uhura does mention her Klingon is a little rusty.
This is the second time in as many films that Chekov has saved Kirk and another crew member from falling to their deaths at the last second, but this time he managed it without the transporter.
Carol mentions that Kirk once dated Christine Chapel, who is now serving as a nurse on a distant space station. Nurse Chapel was McCoy's assistant in the original series (and played by Gene Roddenberry's wife Majel Barrett), and who gets a mention in the Enterprise sickbay during the first film.
The emergency meeting room Harrison attacks early in the movie is located in the Daystrom building.
Though it's seen from a different angle, the Vengeance overtaking the Enterprise at warp, then attacking while still at warp, is eerily similar to the Scimitar doing the exact same to the Enterprise-E.
Enterprise blatantly ignores orders and violates Klingon space.
The construction bay that Scotty finds after being giving Harrison's coordinates looks eerily similar to a Borg Cube.
Spock's violent beatdown of Khan at the end resembles him beating down Kirk in the first movie.
Kirk at one point calls Scotty a "miracle worker". More or less Scotty's title in the original movies (from The Search For Spock onwards).
Along with heavy focus on his very measured deep voice, there were numerous closeups that focused of Benedict Cumberbatch's intense blue eyes and cold stare the opposite of Montalban Khan's very diplomatic and congenial facial expressions. This may be a tease based on the widespread fan speculation that he was being cast as a reimagined version of Gary Mitchell from Where No Man Has Gone Before.
Harrison's freakout when he thinks his crew is dead brings to mind Commander Kruge's when he tires to get his crew off The Enterprise before it blows up.
The Klingon part of the plot (a rogue Starfleet officer who doesn't believe in peaceful co-existence tries to incite a war between the Federation and an alien civilization) is quite similar to the Next Generation episode "The Wounded".
The Enterprise, after being forced to leave warp in hostile space, just happens to do so within shuttle range of an uninhabited planet with a breathable atmosphere so McCoy and Carol have somewhere to work on the special torpedoes.
When the Enterprise comes out of a battle at warp speed, it is stated to be about 250,000 miles from Earth - about the orbit of the moon. Of course the Moon happens to be at that point in its orbit also.
In no time at all they are caught in Earth's gravity and end up in Earth's atmosphere. Now it is possible if the Enterprise was drifting fast it could get to Earth that quickly, but at the speed (250,000 miles in only a few hours at most) it would zip (very unpleasantly) through the only-200-mile-thick atmosphere of Earth and smack into the surface in no time at all, barely having a chance to slow down in the atmosphere and think about their situation.
Cool Starship: The USS Vengeance, a big, jet black Federation warship prototype that is over twice the size of the Enterprise, three times as fast and has about ten times the firepower. Thanks to advanced automation, it also carries a smaller crew complement than the Enterprise and can potentially be operated by one man. Finally, it's the first ship in this continuity that can engage another ship while at warp. She makes quite an impression when the main characters see her.
Scotty (seeing her in dry dock):Holy sh-- Kirk: That's quite a ship you got there, Admiral Marcus.
Crapsack World: The uninhabited province of Qo'noS in which the Enterprise crew track down Harrison appears hellish for humans, and even Klingons don't regularly stop by.
In contrast to most futuristic depictions of Earth these days, averted as per Roddenberry's long-held optimism with regards to Earth itself. Despite people living in huge cities, for example, there are still beautiful areas of countyside such as outside London. And futuristic San Francisco just looks cool, even though Khan breaks Alcatraz.
Crew of One: The Vengeance was designed to need a much smaller crew than its predecessors and could be operated by one person if necessary. This is quite fortunate for Kirk, Scotty, and Harrison when they board it to capture the ship from Marcus then again for Harrison when he truly does have to pilot it by himself later.
Cry into Chest: Uhura cries into Scotty's chest when she follows Spock into Engineering just in time to see Kirk die.
In the trailer. In the final cut, she stands next to him with her hand over her mouth.
The Vengeance lays a severe beating on the Enterprise, enough to knock her out of orbit. It's sufficiently one-sided that the Enterprise never gets to fire a shot as the weapons systems are the first to be taken out. That doesn't stop the torpedoes themselves from being useful, however.
He beats the crap out of Kirk near the film's climax, and it takes him two seconds to deal with Carol and Scotty.
His attack on Starfleet HQ. He spends several minutes hovering outside the window unloading heavy weapons fire into the conference room and laying waste to anyone who stands up or tries to fight back. Kirk finally manages to cripple his gunship only for Harrison to safely beam himself out.
Curse Cut Short: Scotty's reaction to seeing the Vengeance for the first time. He is interrupted by the scene changing to Kirk and Spock entering a room.
Scotty: "Holy sh—" *swish of doors opening on the Enterprise*
On the planetoid, McCoy's hand is stuck in a torpedo counting down to detonation. Carol tries to deactivate it and, failing that, rips out the control unit. Cue torpedo power down.
Carol Marcus valiantly stands up to her father, Admiral Marcus, stating that if he wants to destroy the Enterprise, he'll have to kill her too. His solution? Immediately transport her off the Enterprise to his ship.
Dangerous Phlebotinum Interaction: Exploited. John Harrison's agent destroys the Section 31 weapons lab by dropping a ring he's wearing into a glass of what at least looks like water, causing a tremendous explosion.
Deal with the Devil: Harrison promises Thomas Harewood he can save the man's comatose daughter in the opening of the film. In exchange, Thomas blows up a Starfleet facility shortly after messaging a confession for the bombing (with credit to Harrison) to Admiral Marcus.
Decoy Protagonist: It's actually Spock who defeats Khan, not Kirk. The movie focuses on Spock's growth as a character through Kirk's actions. Unlike most cases though, Kirk doesn't stay dead.
Dedication: The movie is dedicated to the post-9/11 war veterans. Considering the final act of the movie consists of a giant warship leveling half of San Francisco by crashing into it, while in another location military personnel fall to their death in a burning structure, this was probably done to prevent people from complaining.
Detonation Moon: One of the moons of the Klingon home world has apparently blown up.
Development Gag: Carol Marcus initially joins the crew under her mother's maiden name, Wallace. In the early drafts of what became Star Trek II: The Wrath of Khan, the role that eventually became Carol was taken by Dr Janet Wallace from the episode "The Deadly Years".
Disney Death: Kirk appears to die saving the Enterprise, only to be brought back by McCoy.note The scene showed Kirk losing consciousness in the containment chamber, then lying in an open body bag in sickbay. But when McCoy had his epiphany on how to save him with Khan's blood, he put Kirk in one of the augments' cryotubes to preserve his brain function, revealing he was Only Mostly Dead, as commented on by McCoy when Kirk comes to.
Drowning My Sorrows: Kirk after losing the Enterprise, followed by Scotty when Kirk is forced to accept his resignation when he won't allow the experimental torpedoes onto the ship.
Dying Moment of Awesome: Kirk saves the crew by going into the warp core in order to get it working again. What's awesome is that Scotty said the radiation would kill him before he could make the climb; not only did Kirk make the climb, but he kept on going until the damn thing was fixed. And then had enough steam to crawl back to the door again. It may have copied Spock's death in Wrath of Khan, and it may not have lasted, but every fan can agree that Kirk finally got a death worthy of him.
Easter Egg: The music from the Original Series episode "Amok Time" is played very briefly.
Carol tells Kirk that her father, Admiral Marcus, will not destroy the Enterprise while she's on board. Her father agrees... and forcibly beams her out of the Enterprise and onto his ship.
Spock agrees to let Harrison have the torpedoes, pointing out that "Vulcans cannot lie". He didn't say anything about arming the warhead on them, though.
Explain, Explain... Oh, Crap!: Kirk is explaining the possibility of being set up into getting all the captains and first officers in the same room... moments before the room they're in is attacked.
Face Death with Dignity: Spock does this in the opening after getting stranded in an active volcano and insisting that the Enterprise cannot violate the Prime Directive to save him. He's rather annoyed that they do anyway. This becomes a sore point with Uhura later.
Faceless Mooks: All but the commander of the Klingon patrolmen keep their helmets on for the entire scene.
Fan Disservice: During Harrison's attack, we get a upskirt shot of a Female officer as she's screaming in pain.
Fish Out of Temporal Water: Harrison averts this. Despite waking up a few centuries into the future, he seems to have adjusted pretty well. Being genetically enhanced might have something to do with it, and we never see the actual adjusting. Harrison must have been awake long enough to advise Marcus on quite a few matters, after all. The original Ricardo Montalban version didn't seem too have much trouble adjusting quickly, either.
Also, Pike, Kirk's father figure somehow surprisingly survives the first movie. Then, after Kirk is removed as Captain of the Enterprise as a punishment for his behaviour, we have this line:
Pike: They gave her back to me. The Enterprise.
Audience: Ooooh, you are so doomed!
Foreign Language Theme: During the bar scene with Scotty and Keenser, a piece of music played that had different lyrics depending on where it was released. For example, Kyary Pamyu Pamyu was chosen by J. J. Abrams himself to provide the song for the Japanese release, which is titled "Into Darkness".
Khan explains that Marcus' ship, the Vengeance, is constructed so that it can easily be controlled by one person. Khan unsurprisingly uses this feature after the Vengeance's crew is taken out.
A model of the Vengeance appears on Admiral Marcus's desk, alongside several other Federation vessels and early air/spacecraft, near the start of the film.
Khan mocks Spock by saying the latter would never break regulation, let alone bone. At the end of their No-Holds-Barred Beatdown, Spock grabs Khan's arm and breaks it horribly at the shoulder.
Harrison's first appearance is saving Uhura from being killed by a Klingon, due to still needing the crew. Uhura later saves him from being killed by Spock on the grounds that they still need him.
Spock strongly objects to their mission objective of finding and killing John Harrison without a trial on moral grounds, but stands by without a word of objection while Kirk pummels Harrison after accepting his surrender as payback for Pike's death. At the end of the movie, guess who nearly beats Harrison/Khan to death with his bare hands as payback for Kirk's death? Uhura has to put a stop to it both times.
Several times early in the film, characters survive certain death by being beamed to safety. Thus, when Carol Marcus tries to act as a human shield for the Enterprise, Admiral Marcus simply beams her away to his ship.
Spock explains his ability to not break Starfleet regulation and still attempt to preserve a primitive species as "embracing technicality". Spock Prime reinforces this flexibility with regulation when he agrees to tell Spock about Khan, despite the Temporal Prime Directive. What does Spock do when presented with the dilemma of giving Khan back the torpedoes or facing the death of his captain and crew? Gives him back the torpedoes. Just the torpedoes. Hell of a technicality.
Even Scotty gets into the act.
Scotty: Do you know what this is? Kirk: It's a warp core. Scotty: It's a radioactive catastrophe waiting to happen.
Friendship Moment: Subverted. After an argument and being assigned to different ships, Kirk admits to Spock that he's going to miss him, leaving Spock a wide open opportunity to express reciprocation. Spock opens his mouth and...stands there uncertainly for a long moment because he doesn't know what to say, then closes it again as Kirk just walks off in exasperation.
Funny Background Event: When the experimental torpedoes are delivered to the Enterprise, Keenser is seen in the background sitting on one and looking rather taken with it while Scotty is pitching a fit at Kirk.
At the end of the Cold Open, the native casually dropping the sacred scroll as they start worshipping the Enterprise instead.
When Kirk and Scotty meet up with McCoy in sickbay after Spock detonates the torpedoes, Scotty glances down at McCoy's arm and goes wide-eyed. The doctor rearmed all the torpedoes the same way he armed the first one, getting his arm repeatedly caught by the sliding panels.
Harrison's terrorist attack had its own agenda, but its primary objective was to get all the captains and first officers together in an emergency meeting so he could strafe the place and kill as many as possible.
Manipulative Bastard: Admiral Marcus decided to steer Kirk's rage into a course that would ignite a war with the Klingon Empire, first by sending him in a Federation ship to Qo'noS, then by giving him orders to bombard the Klingon homeworld, and finally by sabotaging the Enterprise so that it would be caught by the Klingons.
Admiral Pike accuses Kirk of making reckless command decisions and relying on blind luck to ensure his missions go according to plan without harming his crew.
Harrison guessing that Kirk would decide to capture him instead of just bombarding him from afar, and also guessing that Marcus would come personally to finish him (and all witnesses) off. Which leads to a Xanatos Speed Chessonce the USS Vengeance, which Khan possibly designed to be manned by one person in the event that he could get his hands on it, comes into play.
The only part of Marcus' plan prepared ahead of time were the torpedoes and the USS Vengeance. He did not know that Harrison went to Qo'noS, or that Pike would die during Harrison's attempt on his life, or that Kirk would be agreeable to assassinating Harrison. Meaning that his plan to use the Enterprise to kill Khan and his crew while at the same time provoking the Klingons to war was made up on the spot in less than a minute after Kirk told Marcus of his intentions and Harrison's location.
Out-Gambitted: How Spock defeats Khan, by allowing the latter to retrieve the armed torpedoes he thought contained his crewmates.
General Ripper: Admiral Marcus was making Starfleet more and more military-like, upgrading its armaments (using Harrison), and wanted all-out war with the Klingons, to the point of ordering Kirk to fire into enemy space so as to instigate it.
Marcus knows exactly how charismatic Khan could be, hence his "shit, you talked to him" reaction to when he found out Kirk knew Harrison was really Khan.
Spock has the sense to ask Spock Prime about Khan, which gives Spock the information needed to defeat him.
Kirk knew that Khan helping them was more than likely them helping Khan. This is why he orders Scotty to stun him as soon as they get to the bridge.
Chekov is notably uneasy when asked to don a Red Shirt by Kirk (even the music gives a danger cue). And then, a few scenes later, the joke is reversed: two actual red shirts are told by Kirk to take off their red shirts because they need to go undercover. The two extras look visibly relieved (and, sure enough, they both survive - although, in the novelization, Hendorff dies).
Averted in some split seconds during Khan's slaughtering of Klingons in which we see one get blown in half and another's leg landing near a character, though they're almost out of focus and are shown very quickly.
And played straight as Harrison coldly snaps Carol's leg by stepping on her. We get the bone crunch sound effect and her scream only.
Grand Theft Prototype: Harrison murders Admiral Marcus and seizes control of the Vengeance. Before that he stole transwarp technology from the Section 31 base in London.
Gravity Screw: The artificial gravity inside the Enterprise fails in one sequence, causing crew members to fall relative to the nearby planet's gravity well while the ship twists and turns around them.
Sharp-eyed viewers can spot an Orion woman in the crowd in San Fransisco.
Groin Attack: When Harrison attacks the Klingons, the one holding Uhura promptly lets her go to respond to the new threat. She steals the Klingon's dagger and knifes him in the groin.
The Guards Must Be Crazy: Well, the one who comes upon Scotty on the Vengeance must be legally brain-dead. He's been searching the ship for an intruder that's disabling the weapons and can hear everything from the communicator on the floor, but rather than stunning Scotty on sight he just stands there repeatedly asking what's going on.
Half the Man He Used to Be: As Harrison is blasting away at Klingons with a gun in one hand and a BFG in the other, he uses the latter to completely vaporize the upper torso of one who's attacking Kirk.
Hannibal Lecture: Harrison gives multiple speeches deconstructing Kirk and Spock's motivations and character flaws. Several of these nearly mirror Khan's monologues from "Space Seed" and The Wrath of Khan in tone, though surprisingly avoid any direct references.
Healing Factor: Harrison's blood allows his cells to heal at an astonishing rate, which he uses to heal a sick girl in the beginning in exchange for a favor. Later, Bones revives a dead tribble with it, and then uses it to save Kirk.
Heroic BSOD: Kirk gets 2 of em. First one is after he is relieved of his duties as Captain by Christopher Pike. The second is when Christopher Pike is killed off by John Harrison.
Spock undergoes one when he is unable to give Kirk any advice as Kirk dies.
Heroic Sacrifice: Kirk attempts to sacrifice himself to save the Enterprise. His death is only temporary.
Heterosexual Life-Partners: Kirk and Spock, to the point that Spock gets jealous when Kirk accepts Carol Marcus as a second science officer on-board the Enterprise.
Scotty and his alien assistant, to the point where the alien resigns at the same time Scotty does.
He Who Fights Monsters: The major theme of the film, tying in with Revenge, is the danger of compromising one's morals in the quest for vengeance against those who have wronged you. Kirk's speech in the epilogue states that in trying times, it is even more important to stick to your values rather than become corrupted. This trope is also personified by Admiral Marcus, who becomes an even bigger threat to Starfleet in his attempts to defend it from the Klingons.
Historical In-Joke: The USS Vengeance is described as a Dreadnought-class starship, and a revolutionary new design. In Real Life, the commissioning of HMS Dreadnought, with her powerful steam turbine powerplant and all-big-gun weapons loadout led to a revolution in naval warfare, with all battleships henceforth described as being "Dreadnoughts" or "Pre-Dreadnoughts". Indeed, HMS Dreadnought is the Trope Namer for massive Game Breaker warships being called Dreadnoughts.
Interestingly, it has a second parallel with the original Dreadnought: It wasn't actually that impressive. The HMS Dreadnought only ever sunk one ship in wartime, and it was by ramming it. Likewise, despite the upgrades that went into the USS Vengeance, it is incapable of taking out a single older-model ship (The USS Enterprise).
Although in the case of the original Dreadnought, this was because there was only one major battleship battle during World War One, while Dreadnought was in port in the middle of some refits. Most of both nations' battleships were held back in reserve, the idea being not to risk such valuable assets until the enemy had committed his own.
Hollywood Tactics: The Klingons in Qo'noS focus most of their firepower on Kirk and co. (5 people armed with phasers and using cover) instead of Harrison (one guy wielding a BFG who's standing out in the open in an elevated position). When they engage the latter, they try to run up to him before shooting or use melee weapons, with predictable results.
Hyperspeed Escape: Attempted by the Enterprise, which jumps to warp to flee from the Vengeance, which has her badly out-gunned. This backfires when it's revealed that the Vengeance can catch up with other ships at warp, resulting in Enterprise being pounded by phaser fire until their warp field collapses.
Ironic Echo: John Harrison taunts Spock about his self-control, citing how a man who can't even break a rule would never be able to break bones. Later on, Spock proceeds to beat the shit out of him during his Roaring Rampage of Revenge.
Idiot Ball: Starfleet regulations during a crisis are to gather together their entire fleet command in the same room, which has a huge window overlooking an open area that just so happens to be easily accessible for a small fighter ship. There are apparently no defence measures in place, minimal guards stationed nearby, and nobody monitoring the local air-space for threats.
Kirk, if your Chief Engineer resigns on the spot rather than follow your orders, it's possible that you might be giving terrible orders.
In Spite of a Nail: No matter the universe, Kirk and Khan will always end up at each other's throats.
Insane Admiral: In grand Trek tradition, Admiral Marcus is really a Blood Knight seeking to start a war between the Federation and the Klingon Empire. He has no compunction about murdering loyal Starfleet officers in cold blood.
Internal Deconstruction: Kirk's Field Promotion in the first film from cadet to Captain of the Federation flagship is aggressively torn apart with Pine's Kirk not having the same respect of the responsibilities of the chair as he should. He breaks regulations just in trying to save the inhabitants of the planet and outright lies about what he did in his official report, which is swiftly uncovered by Starfleet and earns him a dramatic demotion.
Spock's Vulcan logic continues to fail him: after nearly allowing Earth to be destroyed by Nero in the previous film, his personal life is now a disaster, with Spock finding himself at sea with Uhura, leading to feelings of neglect. He's not much use when Pike gets shot, either. In fact, it wasn't until Spock completely flipped his wig that he finally got something done.
At the end of the film, Captain Kirk and the Enterprise get sent on the five-year mission. Some viewers have suggested that this was a way of rewarding the hero while getting him and his Doom Magnet of a ship as far away from Earth as possible.
Interrupted Intimacy: Don't think Kirk can top Uhura interrupting his session with an Orion woman in her dorm room? Kirk sees your sexual shenanigans and raises you two Caitians who are annoyed Starfleet is paging him.
Irony: Kirk boasts to Pike that not a single crew member has died since he took command of the Enterprise. Not only will this figure drastically change in the future (so many poor red shirts...), it will drastically change before the movie is over.
Just Between You and Me: Played with. Khan waits until Kirk has been all but fully beamed off the Vengeance before revealing he is going to destroy the Enterprise.
Just Following Orders: Kirk tries to give this excuse on behalf of his crew to prevent Marcus from killing them. Unfortunately, he didn't intend to let them live anyway.
The Vengeance is described by Harrison as "three times the speed" as the Enterprise. According to the novelization of the film, these were identified as "Mark IV" capabilities. They included special modifications to the warp drive and nacelles, that allowed a Dreadnought-class ship to enter the warp tunnel of other vessels. The ship could momentarily exceed all accepted warp factors and catch up with a starship it was following. Now factor in how more heavily armed it is than the Enterprise and how extremely durable it is in design; to the point that it could could remain intact even after the internal detonation of 72 photon torpedoes. Not a ship any captain would want to take on in a straight up fight.
Depending on the retailer, much of the special feature content on the discs is also completely different, angering many fans, who see it a bald-faced attempt by Paramount to get them to buy multiple copies of the film to collect it all.
Loophole Abuse: When justifying his actions to Pike following their semi-botched attempt to rescue a pre-warp civilization without being noticed, Spock insists that they wouldn't have technically violated the Prime Directive had everything gone according to plan.
London Town: The venerable St Paul's Cathedral and the London Eye ferris wheel still stand amongst canyons of skyscrapers, and at street-level, it's clear that what would be 500 year old Victorian buildings are retained and used — as the Star Fleet London HQ, in fact. Out of the city, at the Royal Children's Hospital scenes, it's also revealed that England retains a good deal of picturesque, green spaces. The use of the term "Royal" also implies that, unless the name has simply been retained for historical reasons, the Crown might still exist.
If you look closely, the hospital is actually flying the personal flag of the British Monarch, giving further support that the Monarchy still exists.
Lost In A Crowd: Harrison attempts to escape pursuit by disappearing into a crowd of fleeing civilians.
Made of Iron: Harrison barely even flinches when Kirk tries beating on him as hard as he can. Also, nothing seems to be able to incapacitate him for more than a few moments. It takes a (unsuccessful) Vulcan nerve pinch, a dozen or so point-blank stun phaser hits, a vicious Tap on the Head, then an arm-break, all in rapid succession to finally stun him enough for Spock to get the upper hand.
The Main Characters Do Everything: When Scotty and his assistant quit, fresh out of the Academy Ensign Chekov is made Chief Engineer, over the heads of the rest of the Engineering staff, with nothing but a handwave about him having shadowed Scotty.
Also during the finale. The Enterprise is at Earth. It's pretty obvious they are up against a bad spaceship and bad guys. No attempt is made to contact Earth to put their probably-not-inconsiderable-forces of whatever they can scrounge up (shuttlecraft/tugs to slow the fall of the Enterprise/warning about potentially falling spacecraft) to help.
The scene in which Uhura is walking up to the Klingon war party in an attempt to inform them of their intentions, the camera is firmly focused on her behind as she's walking, right up until she stops.
Similarly, the camera (and Kirk's eye) stealing a look at Dr. Marcus as she changes uniforms.
J. J. Abrams made sure the film was this, as Pretty Boy Chris Pine's ass was cgi'd out of a scene as he "couldn't inflict that on people" (Pine himself was slightly upset about the news), and a Cumberbatch Shower Scene is only on the deleted features (Abrams revealed the existence of the Cumberbatch scene after Trekkies characteristically complained about the Carol underwear scene).
Magic Skirt: When Uhura beams down to assist Spock in an apprehension on a speeding vehicle near the end, her miniskirt doesn't budge in the wind.
The Man Behind the Man: Played With. While Marcus was responsible for bringing Khan back into power, the latter is still the main villain long after the former has left the picture.
Manly Tears: In order, Kirk, Harrison, and Spock, each get a single tear. From the same eye, even. The good guys are looking at the reason for their tears, while the bad guy is looking away from the good guys.
Mauve Shirt: Hendorff, the "cupcake" guy from the first film, makes another appearance.
Two people have called Kirk "son" over the course of the movie. Early on in the movie, Pike cheered Kirk up after he was demoted. Admiral Marcus would later refer Kirk as "son" twice, to speak up during the Starfleet meeting and to convince him to stand down and give Harrison to them. Whereas Pike was genuine and affectionate, Admiral Marcus was more insincere and mocking.
Also spanning across the series, the first and second films end with Kirk entering the bridge of the Enterprise, telling McCoy to get ready, speaking with Spock and as the Enterprise prepares to warp, there is a voiceover.
Meaningful Name: The USS Vengeance is described as a Dreadnought-class ship. The class is named after HMS Dreadnought, a British battleship that made all other battleships obsolete when she was built. The Vengeance is supposed to do something similar to the warships of the non-Federation states in the Star Trek Universe, as it packs much more firepower and much more speed and maneuverability than any other ship in the Federation. Considering how Harrison helped design and build her, the name Vengeance might allude to what he planned to do with her if he ever got the chance. Its name is also similar to the name of a ship from the Mirror Universe episodes of Enterprise, hinting that it stands for something opposite of what a Starfleet ship should.
It's also meaningful plotwise — Vengeance is the kind of name you'd pick for a ship meant to avenge an unprovoked act of Klingon aggression...only it hasn't happened yet.
Vengeance is also the name of a line of Royal Navy warships, which includes a (pre-dreadnought) battleship, an aircraft carrier and a ballistic missile submarine; in other words folks, the name Vengeance has as much historical lineage as Enterprise. Made even more meaningful given John Harrison's British background.
"John Harrison" is also a meaningful name. Like Khan, the real John Harrison performed great service to his Navy (in this case, inventing the marine chronometer, a highly-accurate clock necessary for precise long-distance navigation) and was completely snubbed by them. Granted, the real Harrison did eventually get his recognition, after appealing personally to King George III. Also, he wasn't a complete madman.
Metaphorically True: Given a nod when Spock and Kirk are being dressed down by Admiral Pike. When Spock cites his Loophole Abuse, Pike angrily dismisses it as a technicality. Spock counters that, as a Vulcan, he is aquite familiar with technicalities.
Mildly Military: It's almost startling to see any order actually get obeyed at any point in the film. Kind of lampshaded with the reveal that the Starfleet officers who see it as a military organisation are the bad guys. It's one of the best ironies of the film that Kirk gets a dressing down for not obeying orders because he thinks the rules don't apply to him, and is almost immediately given an order that the guy who dressed him down wouldn't have wanted him to obey, from someone who thinks the rules don't apply to him.
Mind Rape: Of the Brown Note variety. When Spock is fighting Khan, he briefly mind melds with him. Whether Spock just transferred his feelings of grief and rage or did something else, Khan lets go of him and stumbles around a bit before regaining his feet. It seems possible, given Spock's mindset and his previous specific mention of being burdened with them, that Spock transferred the emotions that Pike was feeling during his death as a kind of karmic retribution. It's also possible that, given Khan was attempting to physically crush his skull at the time, Spock was sharing the physical pain he was experiencing at the time.
Spock transferred the impression of the cryotubes with Khan's crew on the Enterprise, showing Khan's just-committed revenge mass-murder to have been pointless.
Missing Man Formation: During the re-christening ceremony for the Enterprise, which doubles as a memorial for all who died, including Christopher Pike.
Never Give the Captain a Straight Answer: Scotty tells Spock to come down and see something... that something being Kirk, before he dies from radiation poisoning. Not only similar to the iconic scene from The Wrath of Khan, but uses nearly identical dialog, too.
Nice Hat: On Earth, Starfleet officers wear visored caps. Except for Kirk, who is far too Mildly Military to remember to actually put his on his head instead of carrying it in his hand.
Nice Job Breaking It, Hero: Kirk stuns a creature that appears before him as he runs from a planet's natives, only for Bones to tell him that the creature was their ride out.
Furthermore, Kirk's lust for revenge is what ultimately dooms the Enterprise. If he had not desired vengeance against Harrison, there would have been no eventual confrontation with the Vengeance. He wanted vengeance and he got it. The Vengeance's merciless assault is what inspires his heartfelt apology to his crew, as seen in the trailer.
Khan's decision to crash the Vengeance into San Francisco and kill countless innocents was probably influenced at least partly by the fact that Spock had tricked him into believing that all of his crew were killed.
Admiral Marcus points out briefly that landing in Klingon territory and taking out several patrols (even in self defense) will still draw the wrath of the Klingons against the Federation. Even though this was his goal to begin with. It's implied this is the reason why the two are hostile to each other during the 5-year expedition of the Enterprise, which starts at the end of the film.
As a furious Scotty points out, by confiscating his transwarp equation, Starfleet inadvertently ended up allowing a rogue Starfleet officer to commit a terrorist attack and then jump across half the universe to safety.
No Celebrities Were Harmed: In an interview with Vulture, Peter Weller compared his character to Curtis LeMay, a figure during the Cold War who was very close to unleashing Nuclear War on everybody, as is Marcus who wants to jump start a war with the Klingons. Lampshaded by Weller.
Bones tells Carol that he once performed a Caesarean-section on a Gorn and delivered octuplets. This may have happened in the interquel plot of Star Trek: The Video Game.
Played straight in the case of the "Mudd incident" referenced when Kirk, Spock and company use a confiscated civilian starship to enter Klingon territory. However, this also qualifies as an All There in the Manual moment, as the "Mudd incident" is actually a major plot point in the tie-in comic series leading up to the movie and a Continuity Nod (see above).
Kirk's apparent past relationship with Christine Chapel that Carol alludes to, but that Kirk has trouble remembering.
No Seat Belts: Averted. While the crew goes without them for most of the film, complete engine failure and freefall into a gravity well is considered good reason to finally use them. They fold out like Sulu's sword in the previous film.
Kirk tries punching Harrison, only for it to have no effect. In fact, Harrison just looks confused and annoyed, and later says Kirk could try punching him until his arm falls off.
Khan shrugs off Spock's attempt at a Vulcan Nerve Pinchand multiple point-blank phaser stun-blasts. It's only after Khan's smacked in the head with a piece of metal and beaten some more that he finally goes down.
Kirk and Bones are involved in a chase scene which ends with them jumping off a cliff into the ocean below.
Harrison escapes the wreckage of the Vengeance by jumping off it.
Not His Sled: The moment Khan is revealed, viewers that saw Star Trek II: The Wrath of Khan are likely to jump to the conclusion that Spock will pull a Heroic Sacrifice again by fixing the Warp Core, complete with his Famous Last Words being mentioned early on as foreshadowing. Nope, it's switched up: Kirk does the sacrifice and Spock watches him "die" through the radiation door.
Not So Stoic: Spock makes it clear to Kirk and Uhura early on that he does feel; it is a conscious effort of his to not feel fear, doubt, etc. His control of his emotions wears down over the course of the film, culminating with him not being able to contain himself when he and Kirk are having (what he thinks is) their last conversation then completely losing it when Kirk dies and Khan is still alive.
Not What I Signed On For: Scotty refuses to bring potentially dangerous prototype missiles aboard the ship, for a military operation he is violently opposed to; when directly ordered to do so by his captain, he resigns on the spot.
One-Man Army: Harrison is a "one-man weapon of mass destruction" who takes on entire Klingon security teams by himself.
One World Order: Subverted. While the Earth's united, there remains cultural and national diversity, with at least some present-day countries apparently surviving into the 2250s. In fact, the Union Jack is still shown flying in London, suggesting that the UK made it as well. While in a bar scene involving Kirk, what looks like an American flag appears to be in the background.
Only Mostly Dead: Kirk, after fixing the warp core by hand. (Well, foot.) Easy to think he is when he was brought to sickbay in a body bag.
When Scotty resigns in protest of their very highly illegal mission to Kronos, he makes a last desperate appeal for Kirk to reconsider and calls him "Jim" instead of Captain.
Spock's reaction when Scotty calls him down to the reactor room. He doesn't even know what happened, only that something terrible has happened to Kirk. He rushes out of the bridge, forgetting to give the legally required order that someone takes command. And as he runs through the halls, there is sheer panic on his face. His reaction to actually finding out what happened is even more unusual; he loses control and becomes violently enraged and vengeful.
Orange/Blue Contrast: Many examples, especially in scenes set aboard the Enterprise. We have orangey faces against blue backgrounds, and sets lit (or painted) in patches of blue and orange.
Overranked Soldier: In the first film, some were left questioning how Kirk "earned" the captain's chair, even though he obviously belongs there in the end. This answers it in the beginning by having Starfleet Command relieve him of command for violating the Prime Directive. It doesn't last long, but still.
Percussive Prevention: Kirk prevents Scotty from following him into the ship's core by knocking him unconscious and even takes a moment to strap him safely into a chair. In a variation, he hits Scotty while he's still vocally protesting the idea on the grounds that the radiation in there is deadly, being savvy enough to know that once Scotty realized he couldn't stop him, he'd try to help him.
Planetville: Nibiru. Apparently the entire Nibiran species consists of the people living around the temple at the base of the volcano. Otherwise the violation of the Prime Directive would be negligible since they were the only ones who saw the Enterprise, and with a massive volcanic eruption going on people living further away would probably dismiss their claims of the giant UFO as hallucinations caused by smoke inhalation. Plus, the Enterprise was submerged under the ocean a short enough distance away for Kirk and Bones to run from the temple to the cliff overlooking that stretch of coastline in very little time.
Pressure Point: Subverted; Spock uses the Vulcan nerve pinch on Harrison, but all it does is cause him considerable pain.
Private Military Contractors: Scotty notes that a guard's uniform doesn't look Star Fleet, but more like a private security uniform. Since the Vengeance is a super-secret ship, probably built by Section 31, he might work for a mercenary firm.
Putting on the Reich: The new Starfleet dress uniforms seem to hint at the undercurrent of increased militarism in the alternate timeline, some of them look like something straight out of the Imperial Navy.
Although, strangely enough, they're now made of denim. The Gap must still exist in the future.
Race Lift: Khan was originally played by Ricardo Montalban, who was a Mexican playing a Sikh. This version of Khan is played by Benedict Cumberbatch, who is English. Cumberbatch does have a line or two sorta-implying that "race" may not traditionally apply to Augments, however.
The Star Trek: Khan tie-in comic series show that Khan was given extensive plastic surgery, a memory wipe, and a fake life history by Admiral Marcus, in an attempt to recruit him into Section 31 as John Harrison, Hero of the Federation. This works out about as well as it did with Michael on Stargate Atlantis
Rage Breaking Point: Spock's emotions are tested enough in this film, and thinking Kirk is dead drives him to total rage.
Reality Ensues: Used in the film's opening. Turns out that when you're a cocky, inexperienced captain of a starship who keeps breaking the rules like Kirk, you eventually get removed from command.
The Enterprise ends up facing a warship, a fast battleship to be exact, that severely outclasses her. She doesn't defeat the Vengeance in combat, gets shot up pretty bad and is only saved because both Scotty and Spock pull a fast one on Marcus and Harrison.
During the space jump between the Enterprise and the Vengeance, Kirk's face mask takes multiple hits from tiny chunks of debris, cracking and nearly killing him.
Red Shirt: Defied when Kirk orders Hendorff ("Cupcake" from the first film) and another security officer to take off their red shirts and put on civilian clothing for the mission to capture Harrison. Both are seen afterward as well.
In the novelization, Hendorff died.
Chekov gets nervous when Kirk promotes him to Chief Engineer, and orders him to "put on a red shirt".
Inverted by Chekov later, when he not only survives the assault on the Enterprise but saves Kirk & Scotty's lives, all while wearing a red shirt.
Played straight though with the crew members down in Engineering that were sucked into the warp field after the bulkhead was breached.
Reed Richards Is Useless: By the end of the film, Bones manages to synthesize a formula from that can effectively resurrect the dead. No mention is made of future use of it, though given it came from the blood of man with now illegal bio-augmentation, it's quite likely its use will be outlawed in the future.
Justified however as it seems work only on the recently deceased who haven't undergone brain death, with the implication that otherwise you'd end up simply as a vegetable (possibly like the Tribble). Likewise since the moral ethics of using Augments for a "cheat death" cure would be highly questionable, not to mention require removing the Augments from cryo-sleep which would be highly dangerous if they woke up, it's likely no-one will dare pursue this line of research.
Knowledge of the "transwarp transporter" technology has now passed from Scotty's hands into those of Section 31, and of course he still works for Starfleet, so there is no reason why they would not pull him from his job as a starship engineer to working on perfecting it for more widespread use. Why go to the trouble of building super-warships and instigating a war just have the means and excuse to destroy a potential enemy when you could just beam a bunch of bombs to the enemy's home planet and sit back and relax as they are wiped out? Also, why make long tedious journeys through space in starships when you can beam almost anywhere in an instant?
Kirk struggles with the urge to vengeance clouding his judgement when it comes to Harrison. Marcus exploits this by thinking Kirk will just carry out the assassination mission and start the war Marcus wants.
As emotions run more deeply in the Vulcan race, Spock comes within a hair's breadth of murdering Khan after Kirk's death, before Uhura informs him they need Khan alive, since his blood can bring Kirk Back from the Dead.
Revenge Myopia: Harrison kills Pike while trying to get revenge on Admiral Marcus, leading Kirk to want to get revenge on Harrison.
Roaring Rampage of Revenge: John Harrison is out to take revenge on the entire Federation for Marcus taking and for all he knows killing Harrison/Khan's crew.
Rogue Agent: Harrison was Starfleet's best agent before a perceived betrayal by his superiors sent him on a Roaring Rampage of Revenge against the entire Federation. It's a cover story for his work at Section 31 and his true identity.
Rogues-Gallery Transplant: Khan, in a change up from the original chain of events, ends up with Spock as his primary adversary in this film. He lacks the grudge that defined him from being marooned by Kirk in the prime-timeline, and ends up spending more time in an Enemy Mine with Kirk than he does fighting him, since without that glaring flaw of It's Personal with Kirk, he can make wiser decisions around him. Kirk still seems to gain his respect as a Worthy Opponent with a similar care for his crew, but this movie might be called Wrath of Spock once Kirk's Almost Dead.
There's an absolutely huge amount of background detail in every shot of Earth, fleshing out the culture, the civilian lifestyle, and generally showing how the world has evolved.
A few of the bar scenes make hilariously great references to 1960s culture, however, giving a nod to the era in which Star Trek was born (and from which much of TOS's set design was drawn).
We get to see a lot more of the internal workings of the Enterprise, including Sickbay and Engineering. Plus, there is a large foyer-like open space in the middle of the saucer section, crossed by catwalks, that have no analog in the original TV or even film version.
Two ships battle in warp space, one knocking the other out. At this point they are 250,000 miles from Earth, as pointed out by dialogue. In the various television series, going to warp in a solar system (or likewise dropping out of it) was treated as dangerous and something rarely done unless necessary. One of their computers would have been alerting the crew that they were near home. It's kind of like driving at 100 miles per hour and stopping on a dime an inch from your house.
Going from Earth to the Klingon homeworld is treated as a less than 5 minute trip, each way. Even Star Trek's own rather vague guidelines on warp speed treat going to the closest star system to Earth, at the speeds the Enterprise is capable of, as a journey taking two days.
The Enterprise's fall to Earth from orbit of the Moon would, as previously mentioned, require her to fall 250,000 miles. The problem is, having her fall that far in the time allotted would require her to be traveling at relativistic speeds, which she clearly wasn't based on how long it took them to pass through the upper atmosphere.
Kirk disobeys the Prime Directive during the film's opening by exposing the Enterprise to a primitive race in order to save Spock's life.
The entire crew also justifies saving the aliens from being wiped out by a volcano by saying it's allowed by 'technicality'.
Spock Prime has sworn never to reveal information from his own timeline to his younger counterpart, lest he alter events any more than they already have been. He makes an exception to explain just how dangerous and untrustworthy Khan is.
Inverted when Admiral Marcus orders Kirk to kill John Harrison in a stealth attack. After much soul-searching, Kirk decides, "Screw the Admiral's questionable orders, I'm doing what's right!" and informs the crew that they will be arresting Harrison to stand trial for his crimes.
Sealed Evil in a Can: Khan; a former Evil Overlord accused of war crimes, and his crew of Augments were cryogenically frozen for centuries in a derelict ship... until Starfleet Intelligence found him. He ends the film this way, too.
Sequel Hook: Maybe, Khan is not killed in the end, unlike his prime counterpart. Instead he's put back into a cryotube.
Sequel Reset: While the movie does justify it storywise, Kirk's character arc from the first movie is effectively ignored and wound backwards just so they can do the whole 'immature Kirk grows and develops into the successful Captain that we all know and love' thing all over again.
The design of Earth's cities now has a very Mass Effect-like look and feel. From the vehicles, to the architecture, you'd have expect to see a derelict Reaper near London. The Klingon ruins suggest a cross between Tuchanka and Ilos.
When Harrison takes out the Starfleet High Command early in the movie, it resembles the scene in The Godfather Part III.
Nibiru, the name of the planet in the opening scene, is the ancient Babylonian name for Jupiter (which has also been used in a couple of different pseudoscientific theories involving planetary catastrophes).
The design of Earth's cities now has a very Mass Effect-like look and feel. From the vehicles, to the architecture, you'd half-expect to see a derelict Reaper near London. The Klingon ruins suggest a cross between Tuchanka and Ilos.
When Harrison takes out the Starfleet High Command early in the movie, it resembles the scene in The Godfather Part III.
Nibiru, the name of the planet in the opening scene, is the ancient Babylonian name for Jupiter (which has also been used in a couple of different pseudoscientific theories involving planetary catastrophes).
The room where the Starfleet captains confer and are eventually ambushed by Harrison looks very much like the archetypal war room seen in films like Dr. Strangelove and Fail-Safe.
Kirk after the attack on the war room and the death of his mentor.
Harrison, whilst talking about how he failed to save his crew.
Spock, after the events in the warp core.
Pike when he dies.
Sinking Ship Scenario: Late in the film, the Enterprise is crippled and tumbling into Earth's atmosphere. Kirk and Scotty make their way to Engineering as Gravity Screw sends them and their fellow crew members tumbling, with many a Red Shirt seen falling to their death.
It's a Small World After All: Both starships just happen to enter the atmosphere of Earth at a distance and angle that San Fransisco is near enough to be crashed into. One ship's computer warns of the difficulty in doing so, at least.
Spanner in the Works: Kirk. By threatening Harrison and offering him a chance to surrender, rather than killing him from afar as ordered, he single-handedly and accidentally derails all of Admiral Marcus' plans. And Spock, who drove him toward that decision.
And Scotty fulfills this on board the Vengeance.
Space Clothes: Averted outside the Enterprise. Fashions from dress uniforms to suits are shown as having developed from their modern-day equivalents.
Speak of the Devil: Immediately after the epic Say My Name above, the Vengeance, now crewed solely by Khan, hurtles past The Enterprise towards the ground, reminding everyone, especially Spock, that Khan still lives.
Superweapon Surprise: What the USS Vengeance was supposed to be. Admiral Marcus planned to use her to blow the crap out of the Klingon warships after they had destroyed the crippled Enterprise. Judging from the reactions of the Enterprise crew when they see her and the events that follow her reveal she definitely would have succeeded in this regard.
Starfleet Headquarters has no defense against hostile aircraft, allowing Harrison to attack the meeting of Starfleet's ranking officers uncontested.
For a supposedly super-secret ship, the Vengeance is inexcusably easy to access. Scotty is able to fly his shuttle right through the main hanger doors with a convoy of supply ships then board it and they never even notice until he's sabotaged it from the inside.
When Carol tells Admiral Marcus he can't destroy the Enterprise with her on-board, he simply beams her onto his ship, then prepares to re-open fire.
Khan threatens to attack the disabled Enterprise unless he gets his crew back. When Spock points out destroying the ship will also kill Khan's crew, Khan replies that he'll just destroy the life support and cut the oxygen. Since his crew are in cryosleep, they'll remain unharmed as the Enterprise crew suffocates.
Spock counters by sending the "torpedoes" to Khan, but arms the warheads in them after McCoy's gotten the cryopods in them out.
Take Me Instead: Kirk pleads with Admiral Marcus to punish him alone and spare the Enterprise crew after disobeying orders and attempting to flee to Earth. Notably, Kirk offered Khan the same deal in Star Trek II: The Wrath of Khan. Khan at least acted like he would accept (and might have); Marcus just laughs it off. Who's the real monster?
Take That: After the cringeworthy scene of Uhura struggling with a Klingon dictionary in Star Trek VI: The Undiscovered Countrynote This is in complete contrast to Uhura's natural grasp of languages, as established in the original series, her counterpart shows her command of the language is far better, albeit somewhat rusty by her own admission.
Taking You with Me: With his crew apparently dead and the Vengeance in no shape to escape or fight, Harrison decides to just ram the thing into Starfleet headquarters. Fortunately for Starfleet, the engine cuts out early and Harrison merely wipes out a small selection of buildings along the coast. Harrison also survived thanks to his enhancements, but Spock was Genre Savvy enough to know he would.
Played straight when Kirk whacks Scotty over the head then straps him into a seat for good measure to make sure he can't stop him from climbing into the radioactive warp core chamber.
Spock does this to Harrison during their brawl, but it doesn't knock him out.
Technology Porn: After all the criticism Abrams got for filming the Enterprise's engine room in the Budweiser brewery in the previous movie, the warp core in this film was shot in the National Ignition Facility at Lawrence Livermore Labs (the same institution where the laser lab in TRON was filmed 31 years before.)
Tempting Fate: Harrison taunts Spock by noting "You wouldn't break a rule, how could you break a bone?" This comes back to bite Harrison in the climactic fight, when a grief-stricken Spock breaks Harrison's arm.
Scotty: Not to tempt fate or anything, but where is everybody? *cue several Mooks*
In the opening, when Spock starts to chew Kirk out for saving him at the expense of violating the Prime Directive and showing themselves to the natives, Kirk brushes him off with a flippant, "What's the worst that could happen?" Cut to the natives, who were earlier praying to the erupting volcano, bowing before an abstracted sketch of the Enterprise—their new God. Made even more amusing by the sacred scroll depicting the volcano that Kirk stole simply getting dropped to the ground and ignored by the native who was holding it.
Kirk gets demoted to First Officer of the Enterprise under Pike for violating the Prime Directive at the start of the film, only to regain his command a few scenes later when Pike is killed and Marcus decides to use Kirk as an Unwitting Pawn.
Scotty resigns from the Enterprise near the beginning of the film thanks to Kirk's sudden bout of obstruction regarding the special torpedoes. He shows up again halfway through the film, and is instrumental in sabotaging the Vengeance.
Kirk's speech at the end takes place almost a year after the Vengeance crash lands in San Francisco.
Transhuman: Notable because of the franchise's attitude towards this subject in the past that a heavily-augmented human (although he could be an android?) appears as a member of the Enterprise crew. Possibly as a minor counterexample to Khan, since he doesn't have any major significance beyond calling out a couple of lines.
Too Dumb to Live: The top Starfleet brass hold an emergency meeting on top of a tower with large open windows. It's not surprising when Harrison attacks them with a gunship.
Trojan Horse: Spock does beam over the 72 torpedos, but Khan's crew are no longer in them and the warheads are active.
True Companions: Played straight, exploited, and lampshaded. Since the events of the last movie, the Enterprise crew has become a family. Harrison recognizes this and exploits it, using his genuine feelings regarding his own crew to gain a small amount of empathy from Kirk. Finally, it is lampshaded when Carol Marcus is welcomed aboard again, establishing that she's been adopted into the Enterprise crew and has a new family after the death of her father.
Spock reveals that he felt nothing on a mission when he thought he was going to die, because he didn't want to think about how much it would hurt Uhura.
When Kirk is dying of radiation, Spock cannot hold back his grief any longer.
Turn in Your Badge: Kirk gets demoted for violating the Prime Directive in the film's opening, and then trying to hide it in his report. Also Scotty gets relieved of duty for refusing to sign for the missiles.
Undying Loyalty: By the end of the movie, it's become obvious that the crew of the Enterprise have developed this with one another after they refused Spock's orders to abandon ship. Even early into the movie, both Scott and Spock continue to refer to Kirk as Captain despite him (temporarily) losing his rank.
Harrison freaks out and tries to crash his ship into Starfleet Academy when Spock detonates the torpedoes inside the Vengeance, ruining Khan's plans and leading him to believe that his people are dead.
Admiral Marcus goes on a tirade about how he's the only one willing to protect the Federation when Kirk tries to have him arrested. Then Khan kills him.
Villainous Rescue: Harrison saves Kirk, Spock, and Uhura's asses from the Klingons, and proceeds to take the brunt of the battle for them, since he knows they've got his torpedoes and he needs them alive.
The Enterprise also would have been destroyed if he hadn't offered Kirk important information about Section 31, and helped them out in general before he decided to destroy the Enterprise.
Violently Protective Girlfriend: Uhura beams into the flying barge with a phaser and fires it multiple times into Khan when it looks like Khan is about to crush Spock's head in.
Spock tells Kirk that it would be unwise to intervene in Uhura's attempt at diplomacy unless they want to incur the wrath of the Klingons... and Uhura.
Visionary Villain: Khan's speech about how the Augments were created to lead others to peace in a world at war.
The War on Terror: The film includes bombings in major population centers and other real world contemporary issues. And, in true, grand Trek fashion, the proper message is that we cannot give in to our fears and devote ourselves to little more than war and militarization, even in the face of "threats". It's in the face of such things that we have to be even more noble, not less.
To say nothing of zipping past another planet—not under Federation jurisdiction—and launching a bunch of missiles at a terrorist hiding there.
Wave-Motion Tuning Fork: The USS Vengeance mounts a pair of these which deploy from the forward hull and target the USS Enterprise. They fail to fire due to Scotty. According to official sources however, they are experimental advanced torpedo launchers, rather than the expected form of this trope.
Well-Intentioned Extremist: Admiral Marcus figured that the exploration-focused Starfleet would not be able to win a war against the Klingons, a war he thought was inevitable. He was only doing what he thought was necessary to ensure humanity's survival. The guy just ends up tapping the Moral Event Horizon when he opts to try and murder Kirk and the entire crew merely for having Khan in their custody, along with other acts.
We Have Become Complacent: Harrison claims the Federation has become an easy target, despite the peace and safety they pretend to have.
Harrison: You think your world is safe? It is an illusion. A comforting lie told to protect you.
Wham Line: "...'John Harrison' was a fiction invented the moment I was awoken by your Admiral Marcus to help him advance his cause. A smokescreen to conceal my true identity. My name is Khan".
What Do You Mean, It's Not Symbolic?: In a movie all about the cycle of violence and the difference between justice and revenge, the super-ship which Khan takes control of is named the USS Vengeance for crying out loud. If Harrison had anything to do with the actual naming, this would probably put Admiral Marcus into Too Dumb to Live.
What Happened to the Mouse?: The two security officers on the away team, the ones that Kirk, Spock and Uhura bring along to arrest Harrison vanish by the time he surrenders, are an ambiguous case. According to the movie, both of them survive (they show up in later shots). According to the novelization, one of them dies (Herndoff, the one Kirk addresses directly about changing out of the uniform). Which is the one we should take as what happened? We don't know.
It's also never revealed what happened to Thomas Harewood's wife and daughter after he blew up Area 31.
What the Hell, Hero?: Kirk gets called out by Pike for falsifying his report regarding his mission to Nibiru in the opening.
Wire Dilemma: Subverted when Bones and Carol try to disarm one of the advanced torpedo warheads to see what's inside. McCoy goes to snip the wire, but the hatch simply slams shut on his arm and the warhead arms and begins counting down to detonation until Carol simply rips a piece of electronics out.
With All Due Respect: The Enterprise is falling into Earth's atmosphere and Spock orders the bridge crew to abandon ship while he tries to save the Enterprise. Sulu answers, "All due respect, Commander, but we're not going anywhere." The True Companions Status of the J. J. AbramsEnterprise crew is confirmed.
A bunch of Klingons (of course) ring it in as jobbers to show how powerful John Harrison is.
And the Enterprise itself, boasted as one of the most advanced ships in the Federation fleet, gets curbstomped by the Vengeance without even being able to fire a single shot back.
Worthy Opponent: Averted. Harrison clearly gains some respect for Kirk after witnessing Kirk's grit and guts in the space jump the two share. He still considers regular humans to be inferior, however, and delivers a beatdown the moment he has the opportunity to, and he unceremoniously dumps Kirk back into that same cell he was being held in before he tries to destroy the Enterprise.