The Most Shocking and Unsettling Star Trek Storylines Ever, Ranked!

Star Trek's heroes have embarked on countless adventures since the debut of The Original Series in 1966. The ongoing journeys of the Enterprise and other heroic starships have showcased humanity's remarkable discoveries and aided those in need.

However, life beyond the final frontier is not always smooth sailing, and the history of Starfleet has witnessed its share of challenging moments. These storylines often emerged as a deliberate attempt to refresh Star Trek for a new generation of viewers, whether through the post-Roddenberry Deep Space Nine or the gritty Kurtzman era. Nonetheless, even the most lighthearted aspects of the franchise occasionally conceal darker elements.

10 The Whale Probe

Many Star Trek fans consider Star Trek IV: The Voyage Home, released in 1984, to be the funniest installment in the franchise. It is remembered for moments such as Chekov's mispronunciation of "nuclear wessels" and Spock's encounter with a punk on a bus, as the Enterprise crew embarks on a lighthearted whale hunt.

However, amidst the comedy, there is a serious threat to Earth posed by the enigmatic Whale Probe. The movie also addresses important issues such as conservation and climate change, which have become increasingly relevant in recent decades. Despite the film's upbeat atmosphere, it serves as a somber reminder that the survival of the human race depends on taking care of our planet.

9 Section 31

Section 31, introduced in the 1998 episode "Inquisition" of Deep Space 9, showcases the dark side of the utopian Federation. Over the years, fans have witnessed this covert organization manipulate foreign politics, attempt genocide, and even recruit dictators from the Mirror Universe - all in the name of the Federation's best interests, or so they claim.

Opinions on Section 31 are divided, with some fans believing that it undermines Gene Roddenberry's optimistic vision of the future. However, the mysterious and unaccountable nature of this organization seems to appeal to Star Trek's writers. Section 31 plays a significant role in the film Star Trek: Into Darkness and the TV show Star Trek: Discovery. Additionally, Paramount has greenlit a Section 31 project with Michelle Yeoh in the lead role.

8 Thomas Riker

Before serving on the Enterprise as Picard's "Number One," William Riker had a fateful encounter on Nervalva IV. The planet's unusual distortion disrupted the transporters of the USS Potemkin, resulting in Riker being beamed back to the ship but leaving behind a duplicate Riker on the surface. This unfortunate duplicate, known as "Thomas," endured solitude for the next eight years until being rescued by the Enterprise-D in 2369.

Seeking a sense of purpose, Thomas joined the Maquis, a rebel group that opposed both the Federation and the Cardassian Union. Taking on the role of William Riker, Thomas managed to steal the formidable USS Defiant from the Deep Space Nine space station. However, his actions did not go unnoticed, and he was eventually apprehended by Cardassian forces. In a selfless act to safeguard his Maquis comrades, Thomas willingly surrendered, leading to a life sentence in a Cardassian labor camp.

7 The Parasite Conspiracy

The "trust no one" theme of The X-Files can be traced back to The Next Generation's episode "Conspiracy," in which a group of slug-like beings infiltrate the highest ranks of Starfleet. Picard and Riker work together to uncover and expose this conspiracy, resulting in a gruesome death for Lieutenant Commander Remmick, who was controlled by one of the parasites.

Despite the Enterprise crew's efforts, the storyline involving the parasites remains unresolved. This is one of the rare occasions where TNG's protagonists are unable to completely eliminate a threat. The true nature of these parasites is eventually revealed in the Deep Space Nine sequel novels, connecting them to the Trill symbionts.

6 Shinzon

The Romulans' actions in Star Trek: Nemesis may lack logical coherence, but they introduce a tragic character named Shinzon. Portrayed by Tom Hardy, Shinzon is a clone of Jean-Luc Picard created by the Romulans as a replacement. Abandoned by the Romulans, Shinzon is sent to the planet Remus, where he endures a life of enslavement in the mines alongside the native Remans.

Shinzon's turbulent past leads the real Picard to contemplate how his own life could have unfolded differently, sparking the timeless nature versus nurture debate. There is even a possibility to empathize with Shinzon's desire to liberate the Remans—until the clone succumbs to megalomania and vows to obliterate the Federation.

5 The Hirogen's Killing Game

In the Delta Quadrant, resides a formidable and ferocious race known as the Hirogen. Their encounters with Captain Janeway's ship, Voyager, throughout its journey back to Starfleet, are fraught with conflict. However, it is in the chilling two-part episode "The Killing Game" that the Hirogen unveil one of Star Trek's darkest plots.

Seizing control of the USS Voyager, the Hirogen employ a cruel tactic by erasing the memories of the crew and subjecting them to sadistic holodeck scenarios, including a simulation set in Nazi-occupied France. Ensign Harry Kim is forced to navigate these harrowing simulations, while the holographic Doctor tends to the repetitively wounded Voyager personnel, inflicted upon them by the relentless Hirogen. This relentless suffering endured by the ship's valiant heroes stands in stark contrast to the typically light-hearted nature of the series.

4 The Xindi

Star Trek has frequently used the franchise as a platform to indirectly address contemporary issues, starting from the Klingon-Federation proxy wars in The Original Series to the exploration of gender in Discovery. During the production of Star Trek: Enterprise, the show was influenced by the tragic events of September 11th and America's war on terror. The show's producer, Rick Berman, deliberately named the antagonists "Suliban" because it bore resemblance to "Taliban."

Later on, the Suliban were replaced by the Xindi, a coalition of aliens aiming to annihilate the human race. In the episode titled "The Expanse," Earth suffers an unprovoked attack resulting in the deaths of seven million people caused by a Xindi probe. In response, Captain Archer's Enterprise is dispatched to confront the Xindi threat. Throughout their journey, however, Archer and his crew succumb to their darker instincts, which include Archer resorting to torture and T'Pol battling her addiction to trellium-D, a mineral with mood-altering properties.

3 The Federation Vs. The Founders

Despite receiving assistance from the Klingons and Romulans, the Federation faced immense challenges in defeating the Dominion and its allies during their conflict. In an effort to avoid defeat, the Federation Council authorized the creation of a morphogenic virus with the intent of eradicating the Dominion's Changeling leaders, a morally questionable act of genocide.

Eventually, the Dominion surrendered after obtaining a cure for the virus. However, this was not the only instance where the Federation engaged in dark treatment towards the Founders. A secret organization known as Section 31 performed brutal experiments on captured Founder prisoners of war, leading to the creation of a new species. One of these transformed Changelings, named Vadic, managed to escape by assuming the identity of her tormentor. Seeking vengeance, she set out to retaliate against the Federation.

2 Nog's Injury

The focus on epic space battles and political schemes often overlooks the real traumas faced by the characters. This may be due to the protective plot armor worn by the heroes, who often appear unaffected by near-death experiences or torture. However, when this protection fails, compelling and darker stories can emerge.

Nog, a beloved character, leaves behind a life of questionable activities to join Starfleet and becomes the first Ferengi to do so. Unfortunately, he loses a leg during the Dominion War. While viewers might anticipate Nog quickly returning to his normal routine after receiving a replacement, the writers of Deep Space Nine took a different approach. They chose to explore Nog's post-traumatic stress disorder (PTSD) in the groundbreaking episode "It's Only a Paper Moon." In this episode, Nog refuses to leave the safety of the holodeck. Although Nog eventually overcomes his ordeal, his story serves as a powerful reminder of the human (and Ferengi) toll of war.

1 Picard And The Borg

The cybernetic Borg, introduced in TNG's "Q Who," are widely recognized as one of Star Trek's most iconic adversaries. Their chilling approach of assimilating civilizations and transforming individuals into mindless drones is disturbing enough, but the true impact of the Borg lies in their effect on Jean-Luc Picard, portrayed by Patrick Stewart.

While serving as the captain of the Enterprise-D, Picard is captured by the Borg and transformed into the formidable Locutus of Borg. Unknowingly, he provides the machine race with knowledge on destroying numerous Starfleet ships. Even after his rescue, Picard remains deeply affected by the experience, as demonstrated in Star Trek: First Contact. Typically composed and level-headed, Picard loses control and expresses his fury when the Borg pose a threat to Earth. He abandons his "more evolved sensibility" and passionately declares that there must be firm boundaries set against the species.

Picard's encounters with the Borg persist, leading to another assault on Earth and the assimilation of his own son, Jack.