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The events in this film and Search for Spock are an elaborate hoax by Section 31.
The Klingon ambassador making claims against Kirk in The Voyage Home is basically correct. A centuries old “Superman” did not nearly defeat a seasoned Admiral with the science vessel Reliant against the Heavy cruiser Enterprise. And no, this alleged “Khan” did not detonate the Genesis torpedo, a weapon of incalculable value, just to spite Kirk. Please.

Kirk’s son, David Marcus, developed the Doomsday Device euphemistically called the “Genesis Device” and Kirk indeed tested detonated the device in the Mutara Nebula.

There was a series of staged battles between Enterprise and Reliant. Reliant’s crew was removed to facilitate the Khan fiction. Enterprise was launched on a “training mission” with mostly trainees. The few officers on board were well aware of the true mission.

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But there were wrinkles. The (rather obviously) non-Vulcan Lt Saavik was a Romulan operative, seeking to sabotage the mission. Her clashes with Kirk over “regulations” were to frustrate the mission. Kirk was RIGHT when Saavik claimed a supposed general order required armed escort for Kirk— there really is no such regulation! However, by this time, he and Spock suspected Saavik was an operative, so let it slide.

Likewise, Saavik continually harassing Spock about lying and secret codes and such were again her simply trying to frustrate the operation.

This is where Kirk and his officers really did repeatedly screw up, in dealing with Saavik. And it was indeed because they all were old and rusty.

Skeptical? Terrell and Chekov are the ONLY people alive who physically interacted with “Khan”. The rest was over com links. Sadly, Terrell was ordered to kill himself when 31 realized the likely Saavik mole. They were trying to beef up the illusion.

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And note that Mc Coy didn’t even put a pretense of scanning Terrell and Chekov when they were found.

The operation went so horribly wrong that Section 31 panicked and attempted to frame Kirk. This is why Kirk appears in the Genesis proposal that previously featured Carol Marcus. Notice how Kirk’s delivery sounds EXACTLY like Carol Marcus’s? It was a simulation anyway, they just swapped in Kirk.

That's not really Amazing Grace.

Saavik is transgender.
  • During the TOS era, it was a general rule that Vulcan male names are some variant of "S___k" (Spock, Sarek, Surak, Sonak, Sybok, only exception being Stonn) and that Vulcan female names are variants of "T'___" (T'Pring, T'Pau). Saavik, however, is a typically male name.

    She is also referred to as "Mr. Saavik" by Spock, who is a personal mentor and has presumably known her for a very long time. Admittedly, this would be considered offensive misgendering but in this case it's likely an affectionately stubborn nickname along the lines of Galen's "Mr. Picard" in "The Chase."

    The major objections would be that Kirk also called her "Mr. Saavik" occasionally and that Saavik was pregnant with Spock's child in deleted scenes from The Voyage Home. The former can be explained by Kirk being a very close friend of Spock who was also in on certain things. The latter is only a problem if you ignore 200 years of future medical advances.
    • "Mr" seems to be some sort of honorary title for crew (helmsmen?) of any gender - it's used for female officers in other Trek series, too. Might be a real-life naval thing.
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    • It's also possible that Vulcans may not see gender as a binary—that they may have more than two genders.
    • It's military tradition to address all persons regardless of gender as "sir" (if superior or equal in rank) or "mister," (if inferior in rank). The "mister" is fairly unusual in fiction because it sounds so odd to civilian ears, but throughout Trek we hear female commanders (Dax, Kira) referred to as "sir," unless they have a specific objection to it (Janeway), so it's likely they maintain the "mister" parlance, we just rarely hear it because they usually use their rank instead.
    • Vulcans' penchant for naming their sons with "S___k" isn't a hard-and-fast rule, it's just a custom to honor Surak. Presumably the "T'P__" tradition for daughters is a similar convention. If Saavik's parents were especially devout in their adherence to Surak's teachings, but found the historical figure whom the "T'P__" tradition honors to be politically objectionable, they could easily have named all their children in memory of Surak, regardless of sex.
    • Saavik was written to be half-Romulan, perhaps explaining the slightly odd name.

The ear slugs from The Wrath of Khan and the aliens from The Next Generation episode "Conspiracy" are the same species; they are also larvae of Species 8472, as a way to explore non-fluidic space like the Founders did.
  • The two aliens look similar and affect humanoids in a similar manner when possessing them. Also, when Species 8472 wanted to prepare their troops for an armed incursion into the Federation, they used a simulation that replicated Starfleet Command to the slightest detail despite having little to no experience with the Federation outside of their encounters with Voyager; the aliens from Conspiracy, however, inhabited the bodies of several top-ranking officers at Starfleet Command. Clearly, Species 8472 sent out babies to non-fluidic space to investigate it as they grew up like the Founders did, but the harsh change in environment stunted their growth to the point where they couldn't mature and had to take hosts to complete their mission; the "mother alien" in "Conspiracy" even mentioned that they only wished for peaceful coexistence, a sentiment shared with the rest of Species 8472 after Janeway convinced them Starfleet wasn't planning on invading their universe.
    • Or they just stole the information on Starfleet from the Borg before Voyager ended their war.

Saavik is the daughter of Spock and the female Romulan Commander from "The Enterprise Incident"
  • I once had a theory that Saavik from Star Trek II, Star Trek III and Star Trek IV was the daughter of Spock and the female Romulan Commander from the TOS episode "The Enterprise Incident", conceived during their oh-so brief time together. It was stated in cut scenes, and I believe in the novelization, that she was half-Romulan, and I thought maybe that commander was her mom.

    Granted, she'd be approximately 17 at the time of Star Trek II, though Star Trek TNG showed Wesley Crusher applying to Starfleet at 15-16, and the new Star Trek film showed Chekov as a ensign at 17, much to McCoy's horror. Even if it makes the Pon Farr scenes in Star Trek III awfully squicky, my theory stands.
  • The Star Trek novel "The Pandora Principle", by Carolyn Clowes, further fleshes out Saavik's backstory, revealing her to be a child of rape who has refused to have her Vulcan parent revealed through genetic testing because she does not want to shame the family (and probably fears rejection). Spock tells her that the Vulcan woman who 'half-raised' her in the prison cell was not her mother, but would have been.

Section 31 destroyed Ceti Alpha VI
  • Firstly, Section 31 was around since the time of Archer, so this WMG would be possible. Now for the how and why. Section 31 is a very paranoid organisation, and wouldn't trust Khan to stay on Ceti Alpha V for long. Afterall, these are supermen. Eventually, they'd get around to building a ship. But they saw a way of preventing Khan from ever rising again, by exploding the nearby planet and the orbital shift hopefully killing everyone off. At the very least, it'd stop then from conquering the galaxy. What they didn't expect was Chekov and co going to the planet and providing Khan with a ship.
    • Wouldn’t Section 31 find it easier to just murder Khan and his crew? Just beam them all up and into the vacuum of space. It’s gotta be easier than blowing up a planet.
    • Also, that's a pretty big screw up for an organization that, in this timeline, is shown to be pretty exacting and cautious. It's one thing for Reliant to mistake one planet for another—the destruction of Ceti Alpha VI seems to have changed the map in the Ceti Alpha System pretty significantly—but there's no reason for Section 31 to make that mistake. And, like the above troper suggests, there are easier ways to kill a group of people in a limited geographical area: Poisoning the water supply, contaminating the atmosphere with that anti-human chemical agent Sisko used in "For the Uniform," a biological pathogen, or just plain old air-bursting a photon torpedo above Khan's settlement.

Ceti Alpha VI is fine and dandy, thank you.
  • We only have Khan's word about what happened to Ceti Alphas V and VI. Since planets don't just "explode" (at least, not to our knowledge), and since Khan has gone completely mad, another explanation might be in order. For instance, it's more likely that Ceti Alpha V was impacted by a large asteroid, perhaps slightly larger than the one that killed the dinosaurs, within a year or two after Khan and his followers were left there (very rare, but not impossible). That would be enough to lay waste to the planet's surface. Ceti Alpha VI is still there, in a similar orbit to Ceti Alpha V, or perhaps even sharing an orbit. When the Reliant entered the system, they scanned Ceti Alpha V, found it to be hostile to life and almost completely lifeless, and assumed it to be Ceti Alpha VI. If they had scanned both planets, they would have realized immediately that something had gone horribly wrong on Ceti Alpha V... but by this time they were physically fatigued and impatient to get this job finished with. An understandable, but unfortunate, cutting of corners.
    • Come to think of it, Khan wouldn't really have been likely to have any idea what did or did not happen to Ceti Alpha IV. An sophisticated starship was having trouble scanning through the planet's atmosphere, so it's hard to imagine an optical telescope would fare any better looking out from the surface. And if you're struggling tooth-and-nail just to survive, how much time are you going to devote to tracking and monitoring the other planets in the system? If they did happen to see the explosion, even if Khan had an astrophysicist in his group for some reason, he'd only have, at best, an educated guess at what they were witnessing—especially if they're limited to the visible spectrum. Unless Khan had access to an orbital telescope or other advanced sensors, he'd have nothing but wild speculation as to what had happened.

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