10 Things That Make No Sense About Star Trek III: The Search For Spock
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The Absence Of Carol Marcus
The film begins with David Marcus and Lieutenant Saavik having left the Enterprise, and the trainees reassigned following the battle with Khan. It's not known where or when the Enterprise managed to offload this crew before limping their way back to the starbase, but Carol Marcus must have been been on the list as well.
David and Saavik join another ship sent by Starfleet to keep tabs on the Genesis planet, but for some reason, Carol is not with them. Since she was the brains behind the operation, it seems extremely odd that she wouldn't be around to catalog the new planet. Instead, David is left in charge of the operation.
9
Kruge Kills Valkris
The iconic Klingons are set up as the antagonists in the very first act of the film, but their introduction is sketchy at best. The female Klingon Valkris is seen hitching a ride on a freighter piloted by what could be mercenaries or spies outside of the Federation. They meet up with a Klingon Warbird commanded by the villainous Kruge.
Valkris uploads stolen data on the Genesis Project to Kruge while admitting that she has looked at it. Kruge decides she knows too much and proclaims her life forfeit. Valkris takes it like a champ, but the entire sacrifice makes absolutely no sense, as Valkris was undoubtedly part of the same cabal of Klingons allied with Kruge in the first place.
8
Valkris And The Genesis Data
It's never revealed exactly how Valkris managed to obtain the Genesis Project data, though many fans have speculated that Federation spies might have gained access to it. This seems highly unlikely given the absolute top-shelf secrecy of the project, not to mention the hoops one had to jump through to access it.
It also doesn't make much sense given the extremely short timeline between the two movies. The interstellar dust had barely settled on the Genesis planet before the entire galaxy seemed to hear of it, which means Valkris would have had to be in multiple key places at exactly the right times.
7
Super-Large Microbes
The Genesis planet's inherent instability meant that biological life would undergo cataclysmic mutations and rapid growth; a side effect of David's tomfoolery. However, that doesn't provide an adequate explanation for the microbes seen clustered together just outside of Spock's torpedo casket.
First, microbes by definition are microscopic. Second, there's no evidence of other life on the planet undergoing rapid size transformations through gross genetic mutation. For instance, Spock ages rapidly from an infant to a young adult in record time, but at no point does he become twenty feet tall.
6
The Video Game
The 23rd century saw a lot of technological improvements, even if the fantastical Holodecks were still a ways off. That makes it all the more strange as to why their digital entertainment hadn't caught up. This is demonstrated in the scene where McCoy visits the local bar.
The patrons are all engaged in drinking, eating, and mingling, but two are busy playing some sort of holographic video game. It makes no sense and looks about as entertaining as an advanced calculus class.
5
The Skeleton Crew
The starship Enterprise is a complex piece of machinery with a lot of moving parts, and they need to be watched over by a skilled crew who know the ins and outs of their respective jobs. This logic seems to fly completely out the window when Kirk and co. decide to hijack the Enterprise and run back to Genesis to save Spock.
Indeed, even Scotty doesn't seem too worried when he remarks that "a chimpanzee and two trainees could run her." This would completely negate the need to have a large crew in the first place, not to mention the waste of materials.
4
Unlocked Starbase Doors
When Kirk and the boys manage to take over the Enterprise, they quickly make moves to leave the starbase and head directly to Genesis. First, they need to get past the space doors, which is a mystery scene unto itself since it's never established how the locked space doors actually open.
The best the audience gets is some banter between Kirk and Scotty, with the latter replying "I'm working on it." No other details are given, and it seems highly improbable that Scotty would have been able to hack or override the space doors remotely. Uhura might have played a part, which is something the novelization suggests.
3
David's Manipulation Of Genesis
Star Trek III reveals that David Marcus attempted to cut corners on the creation of the Genesis Device by utilizing a dangerous element known as proto-matter into the mix. This highly unstable substance had been rejected by the galactic scientific community during the 23rd century, which makes Marcus' use of it particularly head-scratching.
It also doesn't explain why Carol Marcus, the leader of the project failed to see it happening right under her nose.