Ask any Trekkie what the best film in the original movie series run was, and they'll undoubtedly say "Wrath of Khan" without pausing for breath. Indeed, Nicholas Meyer's masterpiece has everything a Star Trek fan could hope for, including excitement, drama, comedy, and of course, plenty of amazing quotes.
It's not perfect, however. Meyer's quest to create a cool follow-up to the divisive Star Trek: The Motion Picture came at the cost of dotting his i's and crossing his t's. As such, there's a laundry list of things that simply don't make sense in the film. Here they are, in chronological story order.
Enterprise Officers Training Cadets
The entire premise of Star Trek revolves around a crew of adventurers in a gigantic starship who explore strange new worlds and meet new civilizations. Evidently, there was some sort of downtime in play, as the bridge officers of the iconic starship Enterprise found themselves training brand new cadets in the Kobayashi Maru test.
It makes no sense for any of these officers to be relegated to such a menial task, to say nothing of the ever-bizarre Kirk himself. It's possible he asked them to join in on the test just for fun, but one can think of a better way for a seasoned Starfleet officer to spend his or her day.
Finding A Lifeless Planet
The plot of the film shifts in the first act and focuses on the USS Reliant, which is on a field mission to locate a lifeless planet suitable to test the Genesis device on. Pavel Chekov served as first officer aboard the Reliant under the command of Captain Terrell.
Chekov's log seems to suggest that they're having significant trouble finding a lifeless planet that meets the test requirements. It's difficult to imagine finding such a planet would be a challenge, especially given that Starfleet has vast space maps of entire star systems to draw upon. Also, it needs to be lifeless. Enough said.
Khan Recognizes Chekov
Star Trek fans know full well that Khan could not, and would not, have recognized Chekov during that first act scene in Ceti Alpha V. It's not possible, and it sets up one of the film's largest plot holes that can be seen from four galaxies away. Nevertheless, no explanation is ever given as to how they know each other.
Khan specifically says that he "never forgets a face," and remembers Chekov's name. In the original popular series episode "Space Seed," Chekov was nowhere to be found, nor was his character even on board the Enterprise at that particular time. The writers clearly forgot to double-check their timelines and chose the one character most ill-suited for this meeting.
Confusing Turbolifts
Early in the film, Kirk shares a turbolift ride with Saavik and they have a brief conversation before a grumpy (naturally) Doctor McCoy joins them. Saavik leaves Kirk and the Doctor to have an exposition moment before the latter leaves.
The outside shot of the turbolift shows the doors closing on McCoy, but it's impossible to tell what deck they're on given the confusing nature of the signs on the wall. It's hard to gauge exactly what the filmmakers were trying to tell us.
The Mechanics Of The Genesis Device
While it's used primarily as a tool to drive the drama of the story, the Genesis Device makes no sense from a logistical standpoint. Never mind the tomfoolery of suggesting that a glorified torpedo could rearrange biological matter at the atomic level and produce a living, breathing planet in no time flat, but there's more to it than that.
The Genesis Project makes no mention at all of the secondary criteria required to even sustain such a planet after transformation - namely its proximity to the sun. From there, one has to take into account orbit, a system's gravity, etc. - all inconvenient to the magic the film is trying to sell.
Khan Wants The Genesis Data
This is one of the biggest and most glaring plot holes in the entire film, by far. It occurs immediately after Khan orders the Reliant to fire on the Enterprise, dealing it enough damage for him to swoop in and reveal himself to Kirk. The two banter for a bit until Khan demands the data for the Genesis Project, which is where things go sour.
The Reliant and her crew were single-handedly tasked with assisting Dr. Marcus on the project, and they would have known the most intimate of details regarding its nature. Yet, for some reason he demands it from Kirk, when Chekov and Terrell are already under mind control and would have easily given it up.
Scotty Carries Preston To The Bridge
After the initial attack on the Enterprise and the subsequent damage that followed, Kirk managed to turn the tables by using the Reliant's access codes to tap into her computer and kick off a counterattack. It worked well enough to drive Reliant off, giving the Enterprise time to regroup and rethink.
Suddenly, Scotty emerges from the turbolift carrying young cadet Preston in his arms, which makes no sense. Why would Scotty not immediately rush him to the medical bay, especially since he's still alive? Had he not deviated to the bridge, Preston might have stood a chance of surviving.
Why Allow Khan To Take Genesis?
After Khan believes he's trapped Kirk and entombed him for all eternity with no hope of escape, he scoots off with the Genesis device in tow, which would have been a big no-no and broken every single rule in the book.
Yes, Kirk was setting Khan up from the beginning, but allowing him to have Genesis when he should have sabotaged or outright destroyed it seems implausible. It's too great a risk for a man so hell-bent on revenge as Khan, and Starfleet would have put Kirk through the wringer for it.
Two-Dimensional Thinking
During the tense standoff in the Mutara Nebula, Kirk and Spock discuss tactics and strategy relating to how they can gain the upper hand against the Reliant. Spock suggests that Khan is susceptible to what he calls "two-dimensional thinking," suggest that the key to beating him is to rely on the Z-axis coordinate of 3D space.
From a purely logical standpoint, this makes absolutely no sense. Khan is not only a genetically engineered intellectual genius, but he's certain to have watched at least one submarine movie in the 20th century, which would have told him that space is indeed three-dimensional.
Why Bury Spock On The Genesis Planet?
The Vulcan race is highly ritualized, and there are a number of rites which must be taken into account following one's death. Yet for some strange reason, the Enterprise crew decides to fire Spock's body out of a torpedo tube so it can land on the Genesis planet as his final resting place.
The fact that there's another Vulcan on board the Enterprise at the time should have sounded at least a few warning bells, yet she makes no mention of it. Naturally, this sets up a conundrum in the next Star Trek movie, which was probably necessary to undo this head-scratching decision while providing a convenient avenue for the fan-favorite character to return to the franchise.