It is perhaps an inevitability, a sad one, that a long-running franchise such as Star Trek is going to drop the ball on some of its plotlines. Not all of the writers have been on the same page, and ideas that perhaps a writer, producer, or director might want to have followed up on, doesn't mean the studio agreed. Unfortunately, in film and television, creativity has to contend with what is practical, or what makes good commercial sense. As much as we viewers may not like it, sometimes decisions are made behind the scenes to keep a show we love commercially viable.
That said, there a number of mysteries and plot holes from over the years that many fans would like to have seen resolved, had the powers-that-be behind Star Trek compromised and allowed it. Fans have tried to fix these in their own personal headcanon, and tie-in media such as Star Trek: Online have made a valiant effort to close the gaps left by the franchise's many unsolved mysteries. However, since nothing in Star Trek that doesn't take place in a movie or television episode is considered hard canon by the license holders, we fans are left to debate and speculate as to what the truth really is behind Trek's unsolved gaffes and untapped possibilities.
Make sure your inertial dampeners are ready and that your replicator rations are stocked. We're going back to the Final Frontier to explore twenty-five plot holes and unresolved storylines from Star Trek's fifty-plus year history.
Originally referenced in "The Paradise Syndrome," the Preservers were an ancient Milky Way race that relocated certain humanoid species or subsets to more protected areas for study and, well, preservation. They used music as part of their language and technology. The possibilities of such a race and the stories of their studies were promising but were not followed up on again outside of non-canon material in Star Trek: Online and novels such as William Shatner's Preserver.
Early in season one of The Original Series, there were a number of recurring guest stars, prominently among them being Grace Lee Whitney as Yeoman Janice Rand. The Yeoman and Captain Kirk were shown to have a mutual attraction and strong tension, something that added conflict to Kirk's command duties. Although there were real-world reasons why the character was written off, no explanation was given onscreen, and Rand wasn't seen again until Star Trek: The Motion Picture.
Established in the second pilot, "Where No Man Has Gone Before," the negative energy barrier surrounding the Milky Way factored into several subsequent episodes as a grave threat.
The barrier was not brought up again in any of Trek's sequel series, nor was its purpose or nature ever explored or postulated on.
There are theories and non-canon stories linking the barrier to a protection put in place by the Preservers, but unfortunately, nothing onscreen has been presented to clear the matter up.
Gene Roddenberry is said to have teased that the machine world Voyager 6 landed on was the Borg homeworld, but there is nothing to substantiate this idea in any canon media. The most we are given in The Motion Picture is that Voyager encountered a world populated by a race of machines that saw it as kindred. Since the probe had no biological components it would not have been akin to the Borg. Spock also mentions that V'Ger had data on whole galaxies, implying it came from somewhere far beyond us... but we'll perhaps never know for sure.
A seemingly throwaway bit of tech made up for this episode, the Enterprise's ion pod supposedly caused the demise of Lt. Cmdr. Ben Finney, landing Kirk in hot water. Why a survey pod that has to be jettisoned during a violent storm is run by a person and not a computer is never explained at all, and the ion pod never resurfaces again for the rest of the series. Convenient for the plot of "Court Martial," but leaves us scratching our heads.
Though meant to be an analysis on aging and how it affects our heroes, "The Deadly Years" ends up creating a conundrum. Although the affliction that ravages the senior staff in the episode is said to be radiation that recreates the effects of old age on its victims, this fails to explain how Doctor McCoy's antidote manages to instantly restore Captain Kirk back to his youthful self, especially since it is based on adrenaline. Maybe that stuff should have been bottled up for later use.
Kirk and Spock went through an incredible amount of effort, at great risk of being compromised by the Romulans, in order to steal a cloaking device in "The Enterprise Incident." Despite being successful, there seems to be no shift in the balance of power, and this dramatic tactical victory for the Federation is swept under the rug (only being spiritually revisited in The Next Generation episode "The Pegasus").
When the Enterprise crew accidentally travels through time twice (in "The [Bare] Time" and "Tomorrow Is Yesterday"), it is shown to be a dangerous, taxing ordeal. However, jumping forward to season two's "Assignment: Earth," Starfleet has gone as far as to order the Enterprise to go back in time for research, like it's just another mission.
Then by Star Trek IV: The Voyage Home, time travel has become dangerous again.
The fact that later in Deep Space Nine we see a hardly secretive Department of Temporal Investigations in operation, suggests a rather casual attitude adopted about time travel. The series can't seem to make up its mind on time travel's dangers.
It takes a fair bit of processing to make sense of Kirk's actions in Star Trek III: The Search For Spock. We as the audience get to see everything happening on the Genesis planet, and know that Spock is alive, but there is nothing onscreen to suggest that Kirk or Sarek for that matter, would know what's going on. That's an important bit of information! We have to assume that before he goes renegade, Kirk is privy to sensitive information about the ongoing Genesis research and what the Grissom crew found, but at face value we have no proof of this and have to go along with it to advance the plot.
The crew of Voyager must wish they had these kinds of warp engines. The troubled Star Trek V: The Final Frontier has the Enterprise-A make it to the center of the Milky Way galaxy in what seems to be hours, perhaps a few days at most. Though the time needed to warp around has hardly been consistent in Trek, this one takes the cake. Some sources don't refer to The Final Frontier as being hard canon like the other films, but until this is confirmed by CBS/Paramount, we're left with an inexplicably fast Enterprise in a story that already has a cargo hold full of problems.
For seemingly no other reason than to create a problem for the crew, Spock ordering a phaser barrage in "The Paradise Syndrome" causes the warp engines to fail.
Scotty says he can't repair them on his own.
Yet the phasers were said to run on charges in "The Doomsday Machine" (on a ship without a working warp drive), and weren't tied to the engines until the Enterprise was refit in The Motion Picture. Even then, one being damaged did not directly harm the other.
In The Wrath of Khan, the Reliant crew is tasked with finding a lifeless planet for the Genesis project and ends up in the Ceti Alpha system. The crew is shown to be tired and overworked, but this is no excuse for Chekov not remembering the system's significance, nor does it spare any embarrassment for no one bothering to check that a planet was missing. In "The Doomsday Machine," Spock was able to notice how many planets were destroyed in various star systems from long range.
After going back in time and bringing back a pair of humpback whales, Kirk and his crew save Earth from a probe that was wrecking the planet.
The whales sing to the probe and everything is grand.
Except no one seemed bothered to investigate the probe further, or try to translate what had been communicated between it and George. The whole movie seems to shrug its shoulders at Earth's peril for the sake of ending the story.
Though First Contact is arguably the best of the Next Generation feature films, its writing left some inexplicable damage on Trek's fictional history. It was already established that the Federation had the technology to wipe short-term memories from people. Obviously, this couldn't be done while the Borg were on the loose, but after the hive was wiped out, no one bothered to think that perhaps Lily, Cochrane, and the others who participated in First Contact ought to not have potentially dangerous knowledge of the future, nor influence from the Enterprise crew.
In "The Squire Of Gothos," Kirk has to deal with Trelane, a high-powered but bratty being who could alter reality at a whim. Sounds a bit like Q... Throughout The Next Generation, the Q Continuum is set up to be the only real set of beings in the galaxy with a high level of nearly omnipotent power, meaning no writer bothered to make any connection between the superbeings encountered in The Original Series and why they all seemed to vanish by the time of TNG.
Although the Romulans would serve as antagonists several more times in The Original Series, the events of "Balance of Terror" seemed to have little consequence. There, a Romulan ship destroyed three bases and attacked the Enterprise while in Federation space, a clear declaration of hostilities. While one could assume that the Romulans wrote that one ship off as going rogue, it does seem quite amazing that a sneak attack invasion would not have provoked more of a change in the status quo.
In "Tomorrow Is Yesterday," the Enterprise crew fixes the damage they caused to the timeline by beaming Captain Christopher back on his plane before it was crushed... except the one that materializes has no knowledge of being on the Enterprise. Also by traveling backward in time, the Enterprise ought to have encountered a duplicate of itself, yet it seems that during the warp, it erased its past self and the timeline-contaminated Captain Christopher in one swoop. Convenient for the story, but not for making sense.
This is a case of plot hole or mystery being retroactively created for nothing. The Klingons' appearance throughout Star Trek's run has changed, but how they appeared in the movies and The Next Generation is purportedly how Gene Roddenberry always intended.
The problem was that the original show didn't have the budget for more exotic makeup.
This turned into a nice in-joke on Deep Space Nine, but subsequent series have tried to make up an in-universe explanation for the discrepancy, creating a contrivance out of what was merely a real-world constraint. Now with Discovery further altering the Klingons, making any consistency out of all these changes is nigh hopeless.
While it's understandable that Starfleet wanted to keep the Genesis Project on the down low, the lack of security measures taken is baffling. A smuggler crew is able to intercept Kirk's report on the Genesis device, and then Starfleet sends the meager USS Grissom out by herself to a dangerous world that is not far from Klingon space. It doesn't help that the Grissom was captained by someone who didn't even know how to order "shields up" when a potentially hostile vessel decloaks behind you.
Data and his brother Lore are considered to be among the most advanced artificial lifeforms known to exist during The Next Generation era. Yet someone seemed to forget about the androids created by the Old Ones in "What Are Little Girls Made Of?" and the entire race of androids that were prepared to seize control of the galaxy in "I, Mudd." Apparently, these synthetic lifeforms fell by the wayside with no explanation, leaving Dr. Soong to later take the credit of bringing androids to life in the Milky Way.
Star Trek: Generations has a long list of problems, but a major one that has lasting consequences for the rest of the film series is the demise of the Enterprise-D. A ship that once stood one-to-one with a Borg Cube was defeated by a lowly, outdated Bird-Of-Prey because the writers demanded it, regardless of whether or not it made sense.
Onscreen, only one phaser volley is fired by the Enterprise and she then turns tail.
The ship unloaded more ordnance against Q in the pilot episode! Even with compromised shields, this a battle that should easily have been won by the Enterprise.
We know that Wesley joined the Traveler on a cosmic journey beyond the scope of what normal humans were capable of. However, we never really found out what exactly happened to him or what kind of adventures he was supposed to be on. We don't even know if he is truly human anymore. Nothing more is seen of Wesley until he shows up as a member of Starfleet in Star Trek: Nemesis at Riker's wedding, as if nothing happened.
Related to the lack of security for Genesis, the Federation and Klingon Empire both drop the ball in Star Trek VI. Their top representatives are meeting at a neutral site for negotiations that will reshape the quadrant, yet the planet is unguarded. The Enterprise battles Chang's Bird-Of-Prey, with no other ships nearby to possibly mitigate the conflict or protect the planet. Surely the Federation President didn't travel by shuttlecraft.
Several times throughout the later Trek series, a ship losing power, and thereby antimatter containment, is a serious matter, as the ship will explode. However, there were multiple instances of starships in The Original Series being totally disabled but still holding the antimatter together (notably the Constellation in "The Doomsday Machine"). You could say that simply no one had thought of the problem until later, but by the same token, the writers responsible didn't bother explaining why it wasn't a problem in the 23rd century.
The biggest problem in Generations is the very force that drives the plot: The Nexus.
It does whatever the writers do or do not want in order to make their story work, regardless of whether it makes sense.
There are a few lines here and there that attempt to explain its nature and why Soran is trying to get back in the way he does, but given how easily Picard resists its influence, the idea of it being pure heavenly bliss doesn't stack up. Worst of all is that the Nexus provides Picard an unlimited number of options to defeat Soran, and we are forced to believe that a man of his intelligence would resort to bringing in Captain Kirk for a fistfight in order to avert disaster, only to get him killed.