The Klingons end up killing the entity impersonating God. Which, if you think about it, is what Klingons did to their own gods! "They were more trouble than they were worth."
While Kirk soundly rebukes the "God", it should be noted there's nothing necessarily preventing it from being the inspiration for deities across the universe. Certainly, it can reach out to psychics across the universe and speak to them or it wouldn't have been able to talk to Sybok.
Spock's uncharacteristic faith in Eden shown in the TOS episode "The Way to Eden" is because he secretly believed in what his brother was searching for.
Why would Starfleet send a starship that's literally falling apart, undercrewed, and generally unready for service to solve the Nimbus III crisis? They weren't sending the Enterprise. It was basically just a taxi for sending James Kirk, the guy who talked his way out of omnipotent aliens, tied multiple computers into knots within 15 minutes of conversation, and has hosted multiple contentious political conferences and delegations. The cult on Nimbus III is about 30 guys armed with sticks and pellet guns, and Starfleet could take care of them in minutes if they approached it as a military problem. They were sending in a hostage negotiator, and just didn't expect him to cut straight to pretending he was playingRainbow Six. They also had no idea Klaa would get in on the action, either.
A possible reason for the numerous problems the almost mint-condition Enterprise-A is having in this movie? It was in Spacedock during the Probe's sojourn to Earth.
Alternatively, Roddenberry suggested it's problems were because it was actually the Yorktown, having been renamed and rushed back into service after the loss of the Enterprise, hence why it comes across as a second-hand ship.
If Scotty knows the ship "like the back of his hand", why does he end up smacking his head on an overhanging bulkhead? Because he was likely thinking of the Enterprise, not the Enterprise-A. Furthermore, it's likely that not all Constitution-class vessels were refit in exactly the same way, particularly if this ship was originally the Yorktown.
Or, maybe while Scotty and the crew were away on Vulcan, Starfleet took steps to ensure that something like what happened in Star Trek III: The Search for Spock never happened again by making changes and modifications that he wasn't made aware of. In other words, all future starships will be "Scotty-proof" to prevent sabotage by even the best engineers. So the ship is "falling apart" as Scotty is trying to undo the changes and return the ship to a state he's more comfortable with.
It's never outright stated, but it's a safe bet that Kirk's greatest pain is the death of his son.
Or Edith Keeler.
Or Spock.
Edith is more likely. When David was killed, Kirk really couldn't do anything to stop it; with Edith, however, he consciously chose to let her die to save history.
William Shatner's behind-the-scenes book Star Trek Movie Memories confirms that Kirk's secret pain was intended to be David's death.
It could very well be all that above with his greatest pain being Khan and either wishing he'd reacted faster when Reliant attacked Enterprise in Wrath of Khan, even further back wishing he'd just killed the potentially dangerous 21st century Supervillain when he had the chance back in Space Seed. Without that Spock doesn't die, Genesis doesn't get activated prematurely and David doesn't go there to get killed by Klingons.
In what is very likely a combination of both Fridge Brilliance and Fridge Horror, there is a lot more going on during the "Row, Row, Row Your Boat" scenes than at first appears. First off, depending on how you look at it, this is either three best friends on vacation shooting the shit over a few beers, or three very lonely work colleagues with few other real friends, no real social life and no family who have no choice but to vacation together. This ties in with the general theme of aging and loss that is running through films 2 through 7 with regards to Kirk and Picard; where you can go on all of these wonderful and exciting adventures, visit incredible planets and meet exotic aliens never before seen by any human, but when the journey is done, you will be coming home to an empty house because the rest of your life has passed you by. Secondly, Bones' anger towards Kirk recklessly endangering his life on the mountain is very likely foreshadowing the revelation of his secret pain later on in the film where he was forced to turn off the life support for someone that he cares deeply about.
Mind you, it's almost certainly just them hanging out because they've spent the better part of 10 years together.
McCoy quite possibly takes this out of the fridge:
McCoy: All that time in space, getting on each other's nerves, and when shore leave comes around, what do we do? Spend it together. Other people have families. Kirk: Other people, Bones, not us.
The theme of aging and loss go all the way back to The Motion Picture, with Admiral James T. Kirk chafing at the fact that while he got Kicked Upstairs, the love of his life, the starship Enterprise, was handed off to Captain Decker, who can come off as a new young replacement for Kirk.
It makes perfect sense Klaa would be snooping around Sol (which is why he shot the Voyager probe). He's trying to get some action and getting into a petty fight with a Federation ship would be just so cool to him. It also explains how he knows there's an emergency — he got the news of Nimbus III from the Federation broadcast, not Klingon.
Sarek never muttered "So human" at Spock's birth. Remember, Sybok is delving into Spock's pain, not memories. Spock's "Well Done, Son" Guy complex is so ingrained he probably feels like Sarek felt that way every second of his life.
Kirk got what was shaping up to be an Unishment at the end of Star Trek IV: The Voyage Home by being demoted back to Captain from Admiral. Having to command a failing ship would make the feeling of punishment stick better.
McCoy defiantly stands up to "God" after he attacks Kirk and Spock for doubting him. In particular, he declares that he doubts any god who'd hurt others for his own pleasure. What could a doctor hate more than someone who harms others for kicks?
Sybok's mother must have been the Vulcan whom Sarek was betrothed to in childhood. It was never addressed elsewhere how Sarek could be married to a human woman when all Vulcans were entered into arranged marriages.
This is the first of the TOS films to be produced after the premiere of Star Trek: The Next Generation. While that show established that Klingons and the Federation are allies in the 24th century (with a Klingon serving on the bridge of the Enterprise, no less), this film shows an early example of the Federation and the Klingons cooperating against a common threat, with Spock convincing General Korrd to get Klaa in hand and help Kirk against "God." This trend would continue in the next film, with the Federation and Klingon Empire deciding to sign peace accords and end their cold war with each other.
Why does landing a shuttle aboard the Enterprise require the use of a tractor beam, when the shuttles are capable of hovering? They should normally be able to just approach the shuttle bay at a comfortable pace and leisurely find a safe spot to park inside. Beyond the danger of a collision if the pilot messes up or one of the ships moves unexpectedly, the next film establishes that impulse engines create thrust, which means they have a backblast. In the confines of a shuttle bay, this could mean folks or equipment getting blasted by the engines, and if the ship itself is underway, the shuttle would likely have to fight its way through the wash of the larger ship's impulse engines. The tractor beam allows the shuttle to be maneuvered without the additional complication of its own engines, and can safely pull it through the engine wash without the shuttle being blown off-course at a bad moment.
Klaa may have done the galaxy a favor in destroying the Pioneer 10 probe. Remember what happened to Voyager 6?
Vulcan infants can remember the moment of their births — is it possible Spock can remember (albeit subconsciously) incidents that happened in utero?
When members of the Enterprise crew sneak into the bar in Paradise City, the Caitian table dancer attacks them. During the struggle, Kirk knocks the Caitian unconscious and throws her into a pool of water. She would probably drown (being unconscious) for doing nothing more than defending her place of employment from nighttime intruders. It's a cruel move by the "good guys", but the movie treats the innocent victim as expendable.
Sybok demonstrates just how terrifying a Vulcan who rejects Surak's teachings can be. While Sybok himself is generally kind and pacifistic, he's nonetheless driven by his convictions to fanaticism, and is unrestrained in his use of his psychic abilities to sway those around him, and assemble an army. It's not hard to imagine the damage a less scrupulous Vulcan (or even a group of Vulcans) could have caused.
Star Trek: Picard demonstrates this on a small scale, with a mind-meld being used to turn an innocent person into a double-agent and assassin.
