The game is split into 8 episodes, each with its own stand-alone story, while together some (but not all) of the missions form a Story Arc.
The recaps below tell the story as it transpires when achieving a 100% score. However, note that unlike Star Trek: 25th Anniversary there are sometimes multiple ways to solve a puzzle that will still lead to 100% score but are not described below, in the interest of presenting a coherent storyline.
The Enterprise is en-route to some educational shore leave, when suddenly they encounter a strange rift appearing in space nearby. Out of the rift comes tumbling the U.S.S. Alexander, a Constitution-class vessel, with obvious signs of damage. Its captain, Luke Rayner, contacts the Enterprise urgently, explaining that his ship has traveled back 8 days from the future, and that the Federation is about to be destroyed. Before he can elaborate, the Alexander explodes.
Tracing the Alexander's path the Enterprise arrives at Espoir Station, a Federation facility researching a nearby phenomenon called Gravity's End where vast quantities of matter and energy from a Big Bang occurring in a parallel universe are being ejected into our universe. Kirk is greeted warmly by the station's commander, Dr. Munroe, and invited to come aboard the station to inspect their work. Together with Spock and McCoy, Kirk beams to the station's bridge.
Upon arrival, Munroe immediately reveals that the station is actually under the command of Dr. Ies Breddell, the Big Bad of the final mission of Star Trek: 25th Anniversary. Breddell has apparently survived the climactic battle against the Enterprise in that game, and is now hoping to use the power of the Gravity's End phenomenon to exact his final revenge against Kirk and the Federation. He traps the Enterprise in an powerful tractor beam, and then orders his Vardaine guards to arrest the away-team, throw them in the brig, and make their stay "as uncomfortable as possible".
In the brig, Kirk strikes up a conversation with his guard, a Vardaine man called Menao Sheme. It turns out that Sheme's father once helped Kirk (then First Officer of the U.S.S. Farragut) elude the corrupt Vardaine government, back when Kirk thwarted Breddell's first scheme to take over Vardaine. Kirk leverages his friendship with Sheme's father, reminds Sheme of his father's strong ethics, and makes him realize that he is working for a madman who is planning to destroy billions of lives. Sheme finally admits that he cannot back Breddell, and agrees to free the away team.
Kirk, Spock and McCoy make their way to the station's computer room, battling the guards as they go. Upon reaching the computer room, they discover that a Vardaine technician had just managed to lock the computer into an endless game of chess against itself in order to prevent Kirk from accessing it. Kirk interferes with the game, mates the computer, and frees it up - allowing Spock to retrieve damning evidence proving Breddell's plans to destroy the Federation.
The away-team retrieves some martial arts training dummies from the station's crew quarters and beam themselves along with these dummies into the station's Security office. The guards in Security detect the transport and open fire at the arriving figures, but the dummies provide enough confusion to give Kirk the advantage, allowing him to stun and apprehend them. He presents the evidence from the computer to the station's Security Officer, Commander Kamend, and convinces him that Breddell's ploy will cause as much damage to Vardaine as it would to the Federation once the Federation's survivors realize what had happened and retaliate. Kamend agrees to stand his guards down and assist Kirk.
Next, the away-team makes its way to the Special Projects room, where they discover a gigantic genetically-engineered monster that had escaped its cell. They are forced to shoot it dead. Nevertheless, they discover the controls for the station's tractor beams and shut them off, freeing the Enterprise. Before confronting Breddell, the team goes to the station's docking bay, where Spock has to use a nerve pinch to neutralize two guards who've remained loyal to Breddell. Once the guards are out cold, Spock empties the shuttle bay of its atmosphere and sabotages the controls to ensure that Breddell will not be able to use the shuttle to escape.
Finally, the team breaks into Breddell's quarters only to find him waiting with a phaser drawn. He refuses to surrender, brushing off Kirk's appeals for morality by stating that morality is an excuse for the meek to pretend that they are superior. Kirk is forced to stun Breddell before he can fire. However, Spock quickly determines that Breddell had already armed his apocalyptic weapon, and that it will soon fire at Sector 001 - Earth.
Scanning Breddell's journal, Kirk discovers a deactivation code written plainly inside. Suspicious of this, he has Spock scan a bookmark inside the book to discover that it contains a different, encrypted code. Spock uses this code to de-cloak Breddell's weapon, which the Enterprise quickly destroys.
Back on the Enterprise, Kirk and Spock discuss the future of Vardaine society now that Breddell's faction has been expelled from power and Breddell himself is safely in Federation custody. Kirk also mentions that Menao Sheme has applied to join Starfleet Academy. While they're speaking, the ship is hailed by the U.S.S. Alexander, oblivious of its fate in the alternate timeline. Kirk invites Captain Rayner aboard to explain to him what had transpired, and what Rayner himself had helped to prevent.
The bridge crew is talking about an up-coming visit to a famous museum of technology on Nova Atar, when they receive a request for assitance from Commander Gellman of the Federation science vessel U.S.S. Demeter. Gellman describes how his ship arrived at Balkos III to study the local primitive, stone-age population, when a routine scan of the planet apparently triggered something that scanned the ship back. Fearing they've triggered some sort of ancient defense mechanism that might attack the Demeter, the ship backed off to a safer position. Gellman asks the Enterprise to come to Balkos III and help solve this mystery.
Kirk, Spock and McCoy beam down to the scanning beam's origin point, deep in a cave under the planet's surface, only to find themselves inside a large and highly-advanced facility of some sort. They explore the unpopulated facility, quickly discovering that it is automatically producing food to lure Balkosi individuals inside, only to hit them with a puff of unidentified gas and release them back to the surface of the planet. Medical examination equipment also indicates that someone was studying the Balkosi here, or perhaps experimenting on them. Unfortunately, most of the machines in the facility are protected by force-fields, and cannot be approached or even scanned properly with tricorders.
Further exploration reveals an automated machine room producing badges and batteries that, when pressed together and recharged, form electronic badges that shut down most of the force-fields around the facility. This allows Spock and McCoy to finally examine the facility's biomedical machinery up-close, and determine that it is producing some sort of powerful pheromone that is being administered to the hungry Balkosi.
Determining what the pheromone is doing to the Balkosi, however, requires the team to knock out and examine one of them as they sneak in from the surface to eat. After doing so, McCoy scans the creature and discovers that the pheromone is making the Balkosi more aggressive. Stranger still, it appears that the Balkosi may themselves be artificial biological lifeforms, specifically designed to make them susceptible to the pheromone they are being gassed with. This fits in with the Demeter's observations, which indicated that the Balkosi may not in fact be native to the planet at all - although it raises even more questions than it answers. Kirk begins to speculate that perhaps the entire facility serves an ulterior purpose than the obvious.
After scrounging up some spare parts littering the facility, Spock manages to repair a console that shuts down the final force-field and allows access to a large computer and the facility's power generator. Examining the computer, Spock realizes that it contains an incredible database of information on how to project three-dimensional holograms - technology that the Federation would find absolutely invaluable. However, he also determines that retrieving this information would trigger the pheromone storage tanks, releasing massive quantities of the pheromones into the planet's atmosphere and thus dooming the Balkosi to a perpetual aggressive state. While McCoy protests vehemently, Spock suggests that perhaps the ultimate purpose of the pheromone is to drive the Balkosi forward on the evolutionary scale, and that the information in the computer database is some sort of reward for releasing it. This further strengthens Kirk's suspicion that the facility is some sort of meta-experiment, and that the away-team is the actual subject of that experiment. Nevertheless, he is reluctant to follow Spock's reasoning.
Finally, Kirk and Spock figure out a way to configure the facility's various parts to interact with each other, so that turning off the power-generator would shut down the entire facility without causing the pheromones to be released into the planet's atmosphere - though this will necessarily also wipe the data in the computer. Kirk decides to go with this plan, freeing the Balkosi to live their lives without outside interference, at the expense of the Federation's own technological development.
Once the away-team returns to the Enterprise, two signals are detected being sent from the planet. One unknown signal is sent into deep space, while the other is directed at the Enterprise. Uhura interprets and displays that second signal on the screen: "SUBJECT SUITABLE. TESTING CONTINUES."
The Enterprise is on its way to an uneventful mission observing some radiation clouds, when a call comes in from Starfleet. It appears that over the past month, ships have been disappearing in the Delphi system. The U.S.S. Zimbabwe was dispatched to investigate, but it too has disappeared. The Enterprise is now ordered to go look for the other ships.
The Enterprise reaches Delphi expecting to find Romulans, but instead encounters what appears to be a World War One era Fokker DR-1 triplane, painted red, being piloted by Trelane - an all-powerful but highly immature being that harbors an unhealthy fascination with the history of human warfare. Now calling himself the "Baron von Gothos", Trelane attacks the Enterprise in his triplane, which turns out to be exceptionally fast and powerful. The Enterprise's skilled crew and captain manage to defeat the triplane, but it simply reforms. Eventually, Trelane gets fed up and puts a stop to the fight by causing the entire crew to fall unconscious.
Kirk, Spock and McCoy wake up some time later inside a locked cellar, which Spock determines is of 19th or early-20th century construction. In there with them is Commander Ellis, the First Officer of the U.S.S. Zimbabwe. With their communicators and phasers disabled, the team resorts to setting the place on fire in order to draw the guards in and enable their escape. Once outside, they quickly realize that they are in the German town of 'Gothos' in the year 1918, just before the end of the First World War. Strangely enough, everyone they meet in the town immediately recognizes Kirk as "Lieutenant Colonel Jimmy Kirk, the famous American flying ace".
It doesn't take long before Spock begins to notice various subtle anachronisms indicating that the entire town is nothing more than Trelane's fantasy made manifest: The characters around them are all trite stereotypes, the town itself is organized in a completely inorganic way, and even the German soldiers controlling the area make no attempt to apprehend Kirk and his team. While exploring the edges of the town, the team also discovers Trelane's triplane parked on a small airstrip, as well as Trelane's opulent castle overlooking the town that is protected by a powerful force-field. Spock surmised that bringing the force-field down would require locating objects of power - similar to the one seen in the Enterprise's previous encounter with Trelane ("The Squire of Gothos") - and destroying them all simultaneously.
The team scours the town for the objects of power. Visiting the tavern, they meet the owner - a young woman called Gretel Gernsbeck - who turns out to be a spy working for the French. They also meet several of the more important members of the community, including Herr Schiller (the local school superintendent) and Herr Sundergard (a local newspaper publisher), and learn their varying opinions about the war and other local matters.
The first object of power is quickly located at the local shoppe - an ornate cuckoo clock - but the team lacks the funds to purchase it. They eventually find work cleaning the house of a one-armed German veteran of the Franco-Prussian War, earning a few coins. Kirk quickly turns the money into a small fortune by playing poker at the back room of the tavern, and uses it to purchase the clock.
As the team explores the far end of town, they arrive at a front-line trench only a short walking distance away. Strangely, the scene is oddly serene and tidy, far from the historical records of the muddy and grim trenches. It also contains only a single soldier - a young man who is severely wounded and kept perpetually on the verge of death by Trelane for dramatic effect. He is holding the second object of power - a locket - but only agrees to part with it after Kirk agrees to deliver a goodbye letter addressed to his girlfriend.
The third object of power proves the most complicated to acquire. Visiting the local school, the team finds a German army captain lecturing the children about the importance of an authoritarian society, while ragging on republics and democracy. Kirk debates the issue and wins over the children's support, causing the captain to leave in a huff. It is then discovered that the classroom's chalkboard is another object of power, but Mrs. Humperdinck, the teacher, refuses to part with it without permission from Herr Schiller, the superintendent.
Schiller is also reluctant to allow Kirk to take the board, even though Kirk claims it may be dangerous to the children's health. Gretel mentions that Schiller believes anything he reads in the local newspaper, so Kirk decides to convince Sundergard the publisher to publish a warning against the use of chalkboards. However Sundergard is also unwilling to publish such a report, but says he would do anything if Kirk could arrange for his son to be taken off the front lines.
To this end, Kirk has Dr. McCoy drug a shipment of ale headed to the local armory, where the tranquilizer knocks out the garrison's Commander and his aide. Kirk ties up the Commander and forces him to sign transfer papers for Sundergard's son at gunpoint. Spock then mind-melds with the Commander to acquire the code to the armory's safe, where the team retrieves some TNT. Spock also explains that - during the mind-meld - he learned that every single person in the town is actually a crew-member of the kidnapped ships, whose minds had been altered by Trelane to become pawns in his little dramatic piece. After giving the transfer orders to Sundergard and getting the smear published in the newspaper, Schiller agrees to hand the chalkboard over to Kirk.
Throughout the search for the Objects of Power, Ellis proves to be little more than a Load, constantly criticizing Kirk and sarcastically pointing out places where he (wearing a Red Shirt) might be ordered to die for the team. Kirk eventually confronts him on this, discovering that Ellis was friends with a man called Ralph Garvin who was killed by a blood-sucking cloud under Kirk's command. Ellis has thus concluded that Kirk is a callous leader who simply throws away the lives of his men. Kirk does his best to argue with Ellis, and tries to explain that he is haunted by the death of every single subordinate- but Ellis refuses to change his mind.
With all objects of power in hand, Kirk places them into Trelane's triplane and blows the whole thing up with the TNT. This prompts Trelane to transport them instantly into his chambers in the castle. He gloats over Kirk, claiming the Kirk is his arch-enemy and that this is the day of his final defeat. On the mantelpiece over the fireplace, Kirk spots bottles containing the three kidnapped Federation ships as well as the Enterprise - all shrunk down and immobilized.
In the "canon" solution note , Kirk points out that Trelane's recreation of the First World War trench-line is highly inaccurate, and convinces him to create a more accurate depiction based on the Enterprise's computer records. Trelane transports himself and Kirk into the new recreation, which is exceptionally grim: full of mud and soot and blood, as well as the many shredded bodies of the poor German and French soldiers. Kirk then launches into a speech explaining how gruesome and unglorified the actual war had been, and how the patriotic calls for war quickly turned into a terrible bloodbath where even the winners paid an unthinkable price. Eventually, while he does not truly manage to make Trelane sympathize, he does frustrate Trelane's sense of self-satisfaction and his fascination with Earth's wars. Trelane finally releases the ships and their crews.
Kirk is returned to the Enterprise bridge where he talks with Spock about the horrors of the realistic battlefield. Kirk also reveals that he ended up solving his argument with Commander Ellis over a match of Zero-G Squash, which Kirk essentially lost. Nevertheless, Kirk says he wants to ask Starfleet to transfer Ellis to the Enterprise. Before the mission is over, a familiar young woman enters the bridge and reveals that she is in fact Gretel Gernsbeck, Captain of one of the kidnapped ships. Though she has only a vague sense of meeting Kirk during the mission, Kirk does seem to imply that he would like to meet her again in a more intimate fashion.
During a routine starcharting mission, the Enterprise receives a surprising distress signal from a nearby planet previously thought to be uninhabited. The planet, Onyius II, is itself an odd phenomenon: A highly improbable Class-M planet in a very inhospitable star system. Upon arrival they scan the planet, detecting exactly two life-forms on the surface within very close proximity to one another. Kirk, Spock and McCoy beam down to investigate, along with an expert geneticist - Ensign Jons - who is brought along in case of a First Contact scenario with a new type of life-form.
The planet below is bleak and barren, but the transport puts the team right next to a large stone structure standing alone in the landscape, surrounded by an array of dish antennae. Scans reveal that the building has been standing there for 50,000 years, though it has suffered surprisingly little damage from the constant micro-meteorite impacts. The antennae, on the other hand, appear almost brand new. Scans of the large doorway into the structure reveal that it was sealed with a force-field until very recently.
Inside the building is an impressive genetics laboratory, with equipment that is on par with cutting-edge Federation technology. It appears fully functional and undamaged, despite scans showing it is nearly 50,000 years old as well. Exploring one of the adjacent rooms, the team discovers a machine that suddenly comes to life, and before them appears the visage of a golden glowing angel, twice as tall as a man.
The visage speaks to the team, saying that its name is Azrah and that it represents the Omegans, one of the two species on this planet. Azrah beseeches Kirk to help the Omegans rid themselves of their mortal enemies, the Alphans, which he says are also here inside the building. He also warns Kirk not to heed the words of Vizznr, the leader of the Alphans, whom he says is deceitful. Kirk explains that the Prime Directive prohibits interference in other races' wars, but promises that he will work to negotiate a compromise between the two species. Azrah is highly doubtful, but asks Kirk to report on what transpires with Vizznr.
While this conversation is going on, Spock and McCoy make scans of Azrah and the machine in this room, determining that Azrah is nothing more than an artificially-intelligent projection. The Omegans of which he spoke are a colony of single-celled organisms living inside the machine, which is equipped with enough food to keep them alive for eons. However, McCoy also determines that the Omegans have a healthy metabolism and long life-span, but their reproduction rate is abysmally low. Meanwhile, Ensign Jons expresses great enthusiasm about Azrah, speaking of him as an angel incarnate, and supporting his claims wholeheartedly - imploring Kirk to help the Omegans destroy their enemies.
In the room on the other side of the lab, the team discovers another identical machine. This time, they are met with the image of a monstrous creature, ugly and dripping, which identifies itself as Vizznr - leader of the Alphans. Vizznr claims that the Omegans came to this planet and attempted to destroy the Alphans, and asks Kirk to help protect the Alphans from them. Kirk ignores the creature's hideous appearance - even noticing how passive it is compared to Azrah's blood-thirstiness - but once again cites the Prime Directive and asks Vizznr to agree to a compromise. Meanwhile, Ensign Jons is disgusted by Vizznr, claiming him to be a foul demon whose lies must not be believed - to the point where Kirk has to order him to stop interjecting his opinion into the conversation.
Scanning the Alphan machine, McCoy determines that the Alphans are also single-celled creatures, but that they reproduce at an extremely high rate and have a very short life-span. Kirk surmises that these creatures may have been separated somehow, each having only part of the positive traits of some original species. He manages to convince both Azrah and Vizznr of this, and they each provide a sample from their respective colonies.
Kirk orders Ensign Jons to use the genetics equipment in the laboratory to combine the two species together. However when Jons inputs the Alphan sample into the machine, the sequencing process fails. McCoy offers to help, but Jons rejects his help vehemently. Spock and Kirk become suspicious and confront Jons, who claims that he is doing what's right by protecting the "perfect and pure" Omegans from being tainted by the "evil" Alphans. Kirk calms him down, and points out that Azrah and Vizznr are simply holographic images that have nothing to do with the single-celled creatures that they are trying to combine, and that both holograms agreed to the reunion of the species anyway. Eventually, Jons is convinced to look past their appearance. He merges the two species together, creating a new species which he calls the "Gammans".
The team discovers a third room inside the facility containing a machine similar to that in the other rooms - but empty. This machine is designed to incubate a species until it can be released unto the planet's surface. McCoy inserts the Gammans into the machine, and it turns out that they are a strong and viable species. Once inserted, the machine comes to life and displays another hologram, which looks like a chimera of Azrah and Vizznr. The hologram, calling itself Cicissa, begins to speak with Kirk, but seems to be stuck in a loop. Kirk contacts the Enterprise to determine whether Cicissa's image is actually being projected from elsewhere, and Uhura confirms this. She says the signal is coming from somewhere else in space, and is being received outside the facility.
The team inspects the antenna array, discovering that one of the dishes is standing on some rock that has broken away, misaligning it. Re-aligning the dish requires restoring power to the control console, which is normally powered by geothermal energy. McCoy suggests using the Enterprise's phaser banks to fire a microwave beam at the nearby rocks, creating the necessary energy. After this is accomplished, Scotty uses the ship's computer to calculate the dish's new alignment, which Spock inputs into the array.
Once the dish is re-aligned, the team returns to Cicissa, who now explains the entire affair. He confirms that Azrah, Vizznr and himself are nothing but holograms created based on human sensibilities, and have nothing to do with the single-celled Alphans, Omegans, or Gammans. He says that the facility was built, many thousands of years ago, by a species known as the "Brassica", as some sort of test of reasoning capacity - pointing out the disparity between the "angel's" and "demon's" words and their behavior. He also indicates that this test has to do with a species' ability to ignore its traditional beliefs and customs when dealing with new situations. Cicissa mentions that similar tests are currently proceeding at sixteen other locations - and that most of them have failed - but that Kirk and his team have performed "admirably". He wishes them good luck on their continued quest, and disappears.
The Enterprise enters the Antares Rift, and quickly runs into various problems. Particularly, the warp engines need to be taken off-line to prevent them from suffering serious damage. As the crew tries to cope with the various technical issues, a powerful burst of energy strikes the ship, disabling most systems. Spock determines that the Rift must contain many tears in sub-space, possibly leading to other dimensions. Unfortunately, the explosion has rendered the Enterprise's main bridge sensor controls inoperative, and has also blocked the turbo-lift. Spock convinces Kirk to allow him to beam directly to Auxiliary Control to get the sensors working and navigate the ship out of the Rift.
When Spock attempts to transport out of the Bridge, instead of beaming out as normal he suddenly disappears in a flash of light and electricity. In his place appears some sort of four-armed, grey-skinned alien, who also disappears after a short moment.
The Enterprise engineering team clears the bulkhead, allowing Kirk, Sulu, Chekov, and Red Shirt Ensign Walker to leave the bridge, headed for Auxiliary Control. When they get there, they find the four-armed alien inspecting the control consoles. They barely manage to get a medical scan of the creature before it teleports them suddenly outside of the room and locks the door behind them. Kirk hurriedly takes the scan to McCoy, who determines that the creature is a female Vurian - the only known living member of a long-extinct race. He manufactures a canister of gas that should specifically knock out Vurians.
Kirk inserts the gas into the Enterprise's ventilation system in Main Engineering, and has Chief Kyle transport the team into Auxiliary Control, where they witness the creature struggling with the gas and eventually teleporting away. Using the ship's scanners, they determine the creature's destination was inside one of the space-time rifts. The away-team transports into the rift in pursuit, hoping that this will lead them to Spock.
At the destination, Kirk and the away-team find themselves in an alien dimension, a small flat plain littered with colorful rocks and minerals, and surrounded by a completely empty void. Unable to contact the Enterprise, they resolve to keep looking for Spock. Scans quickly determine that all matter within this pocket-universe is organic - including the mineral-looking rocks and even the ground itself.
After a short search, the team finds the Vurian, still struggling with the effects of the knock-out gas. She calls herself Emminata, and tells Kirk how she attempted to escape the war that eradicated her home planet by making a dangerous maneuver with her ship, only to find herself transported into this alien dimension where she crashed. According to her, she was saved by an entity calling itself "the Savant", which melded with her thanks to her minor psionic abilities and has been keeping her alive and in a state of pure joy ever since. She claims that her visit to the ship, on the orders of the Savant, was only intended to extract Spock and prevent the others from following. She did not intend to cause any damage.
Some distance away the team discovers a massive hole in the ground, surrounded by the wreckage of Emminata's ship. From the hole erupts a great beam of light - the Savant, a disembodied entity of pure emotion. The Savant describes how, a million years ago, it got fed up with the humdrum of physical existence and the hardships of corporeality, and turned itself into this entity so that it would never have to feel unhappy again. It insists that eternal joy should be the desire of any living creature, and that it kidnapped Spock only in order to give him this "gift". The Savant expresses sympathy for the danger the Enterprise is in, and offers to return the away team there and clear the way for the ship to escape the Antares Rift. Naturally, Kirk refuses to leave without Spock, and the search continues.
Spock is finally located at the far end of the pocket-universe. He is clearly struggling with the mind-meld forced upon him by the Savant. Being Vulcan, he has conditioned himself to feel no emotions - but is now being forced to experience them anyway. He theorizes that the Savant is a creature that has become addicted to happiness, and needs Emminata and Spock to generate happiness for him to feed on. In his current state Spock can offer very little assistance to the team, but does reveal that the strange minerals encountered on the surface of this universe are in fact the Savant's negative emotions being excreted as a physical waste-product.
Kirk and the team collect some of the minerals, experiencing a wide variety of powerful emotions as they do so - nearly leading to violence among them. Kirk makes one final attempt to convince the Savant that forcing other creatures to experience anything - even if it is notionally a "good" experience - is morally wrong. When the Savant refuses to concede, Kirk throws the emotion-rocks into the Savant, destabilizing its state of joy. Only then does the Savant relent, and releases the away-team - Spock included - back to the Enterprise.
Kirk, Scotty and Chekov beam down to the museum. They are unarmed and unequipped, due to the Smithsonian's policy of "no external equipment allowed." They tour the museum for a while, waiting for the ceremony to begin, discovering many interesting exhibits all related in some way to future-historical technology and engineering. Scotty is particularly excited, discovering many objects he remembers from his youth or has only heard about. The team also gets to see the probe that is about to be gifted to the Seransi, under heavy guard.
The team is soon recalled to the curator's office, where he breaks out his family's prized cognac and proposes a toast to the Enterprise. Just then, alert klaxons go off, and the security monitor shows terrorists taking over the probe's exhibition room - locking the door and shooting out the camera. When the curator attempts to activate the museum's defenses he triggers a Booby Trap that was hidden in his security console, and is knocked out. All access to the museum's security systems is then severed.
Scotty manages to pull up a schematic of the museum, and figures out that the terrorists will be attempting to tunnel out of the museum and would take about two hours to do so. The team searches the curator's office and finds a passcode hidden behind an ancient decanter of cognac, allowing them to leave the office into the museum itself.
The door to the next part of the museum malfunctions irreparably, forcing the team to devise a way to get through. Examining the exhibits, Scotty suggests building a make-shift mass driver to punch a hole through the door, which the team does by scrounging various parts from the ancient exhibits. They use a steel lance from a suit of armor in the curator's office as the projectile, levitating it on a set of powerful docking magnets and firing it at the door, which shatters to pieces.
In the next part of the museum, just outside the room with the terrorists, the team discovers two different ways to break in: A small transporter unit, or an old communications device. Both machines are missing parts and power sources, forcing the team to continue cannibalizing the museum's exhibits to repair them. Eventually they are faced with two options: Either try to beam a small canister of Knockout Gas into the terrorists' room, or attempt to contact the Enterprise on the comms console. Scotty advises against using the transporter, however, due to it being a dangerous and unreliable model that could fail to achieve their goals.
Kirk decides to opt for communications, but when he tries to reach the Enterprise he instead makes contact with the terrorists themselves. The speaker, a man called Lucas, explains that he comes from another family on Lachian that is being oppressed and silenced by the Seransi. He claims that the Quelque (the probe being gifted) belongs to all Lachians as part of their heritage, and blames the Federation for backing the Seransi. Kirk vehemently denies Federation partiality, explaining that they had no idea that the Seransi were oppressing anyone's voices. He guarantees to Lucas that the Federation will not give the Quelque to anyone until fair arbitration can be arranged. Lucas finally agrees, opening the door and ordering the other terrorists to surrender their weapons.
(This mission opens with an optional encounter: A Distress Signal from the Romulan Neutral Zone in which a Romulan ship asks for assistance. If Kirk decides to violate the treaty and enter the zone, the Enterprise arrives there only to be attacked by a rogue Romulan warbird that was hoping to lure in a Federation ship. After the battle more Romulan warbirds arrive, but their commander assures Kirk that they will ignore the Enterprise's treaty violation as the ship was only responding to a distress signal, and had incidentally also helped rid them of a rogue captain. The Romulan takes the opportunity to grill Kirk about the Brassica - whose tests the Romulans have apparently also encountered - but Kirk manages to hide his knowledge of the alien race. The Enterprise is allowed to return to Federation space unharmed.)
The Enterprise receives a Code One Distress Signal - a planetary catastrophe - from the planet Atabis III deep inside the Klingon Neutral Zone. It appears that a massive spaceship of unknown origin is about to land right on top of a Federation colony on that planet. Upon arrival, the Enterprise encounters a Klingon ship already on the scene. Its captain, Klarr, assures Kirk that he means no harm to the Enterprise nor the colonists below, and is only interested in exploring the alien ship itself. Kirk agrees to stay out of the Klingons' way during the mission, so long as mutual respect is observed by both teams.
Kirk, Spock, McCoy and Uhura arrive on the alien ship, and quickly determine that all of the passengers on board are mentally-damaged in some way - most of them refusing to interact at all, and others entirely unaware of what their ship is doing. Many seem to be developmentally-challenged or insane to varying degrees, though none are outright violent. At one point, the team finds the ship's sleeping area, where Spock speculates that the ship is a sleeper-ship designed to carry passengers in stasis for a long voyage of some sort. After that, the team discovers what looks like a kindergarten-style "play room" that was taken over by an exceptionally paranoid passenger called Tuskin and his two burly (but mentally challenged) bodyguards Gormagon and Rackaback, who threaten Kirk with violence if he tries to get in. When Spock pulls out a tricorder, Tuskin becomes extremely agitated, believing that the scan will "alter his mind". Nevertheless, the scan reveals that the playroom is hiding some sort of spatial anomaly that Spock is very intrigued by.
Exploring the ship turns out to be somewhat difficult and confusing, with rooms being arranged in a way that seems to defy reality - as though the ship curves into itself. Nevertheless, they finally discover the Oratory - a room seemingly designed for the passengers to learn from the ship's central data library. In this room the team is scanned and then addressed by the ship's on-board AI, calling itself the "Phays". To Kirk's surprise, the Phays itself appears to be "mentally damaged" and illogical. It believes that the away-team members are simply some of its passengers, treating them like children and repeatedly suggesting that they go eat something. It refuses to address Kirk's pleas to stop the ship from landing on Atabis III, claiming that it is simply returning to its point of origin as planned, and that the planet below is its homeworld that is awaiting its return. Spock notices that the Phays is providing contradictory information, but all attempts to convince the Phays to accept the reality of the situation fail.
In the same room, the team finds an old woman lying on the floor in a catatonic state next to a destroyed computer terminal. Spock mind-melds with the woman to try and determine what happened, revealing that she was obsessed with learning all of the information from the computer to try and make sense of the situation. When Tuskin came in one day and destroyed the terminal in a fit of rage, the woman went into a state of shock from which she will never recover. As this is going on, two Klingons finally beam aboard the ship: Captain Klarr and his aide. The aide is furious and accuses Kirk of trying to extract information about Klingon territory (through which the alien ship passed on its journey) from the woman's mind, but Klarr displays uncharacteristic patience and allows the mind-meld to proceed.
Exploring the ship further, the team discovers a medical laboratory that also functions as an eating area. A food dispenser here is producing pre-packaged meals that are heavily dosed with tranquilizers - leading McCoy to conclude that the Phays is drugging everybody to keep them docile. In the room is a distressed woman named Moll, who claims that she let her son down by destroying the ship's hydroponics bay. She says she used to give her son fruit from the plants so that he wouldn't have to eat the medicated food, but that one day the plants started dying. Kirk promises to look into this situation.
Next door, Kirk finds the hydroponics bay which is teeming with plants, but the one plant that can bear edible fruits is indeed dying. After some examination, Spock discovers that the machine is simply clogged with some bacterial growth which is easily removed with a phaser. However, the plants will not grow without nutrients, and the nearby workbench that is supposed to supply them is malfunctioning irreparably. The team scours the ship for suitable minerals, and finds one passenger - Jakesey, an adult with severe developmental deficiency - is playing with toy-like blocks that contain all of the required minerals. Unfortunately, he is unwilling to give them up.
Back in the playroom, Spock beats Gormagon - the smarter of Tuskin's two bodyguards - in a game of chess, and wins a teddy-bear. Kirk hands the bear to Jakesey in exchange for the blocks. The blocks are then placed into the hydroponics fertilizer keg, and the plants come back to life within minutes and bear a tasty fresh fruit. Kirk gives the fruit to Moll's son Stambob, winning his and her trust. Stambob gives Kirk some rotten fruit he had kept hidden, which McCoy uses to distill a powerful sedative. Kirk drugs a pre-packaged meal from the food dispenser with the sedative, and convinces Moll to offer this food to Tuskin - since she is the only person he accepts food from.
Finally, Kirk goes to the playroom and offers a meal to Tuskin, who calls for Moll. She gives him the drugged food instead, and he falls asleep. Kirk uses this opportunity to stun Rackaback, and convinces Gormagon that they are only here to help. Gormagon agrees to reveal the playroom's secret - an access tunnel leading into the heart of the ship. The away team and the Klingons make their way down the tunnel, to find themselves inside the Phays' computer core. Unfortunately, it too is damaged.
The away team returns to the living area, scanning for components that could help in the repairs. Spock discovers them in a lighting fixture hanging over a makeshift throne, but the occupant of the throne (an old man dressed in a paper crown and cape) refuses to budge or even speak with the "peasants" before him. Uhura manages to convince him that she is of Royal Blood, and that she will look after his possessions if he wants to go to sleep - which he does. Spock dismantles the light fixture and the team rushes back to the Phays' interior.
After the Phays is repaired, it seems significantly more coherent. It immediately agrees to stop landing on Atabis III, and begins to answer questions. Firstly, Klarr asks the Phays to surrender any information it has about Klingon space (which his aide demands aggressively, much to Klarr's chagrin), and makes an offer to additionally purchase the rest of the Phays' secrets. Kirk is more interested in the Phays' true origin, the nature of the "Builders" and the purpose of the ship itself - but the Phays gives only vague information and finally directs Kirk to read the computer's library for more detailed answers. However, after Kirk reads some of the more pertinent library entries, he quickly realizes that the library does not in fact contain any more information than the Phays had supplied. Suspicious, he confronts the Phays about this.
The Phays takes a few seconds to think, and then announces that Kirk and his team have passed the final test, and that they are now ready to meet the Brassica. It opens a dimensional portal inside the room, but says that anyone may refuse to enter the portal and just go return to their ships if they so desire. Klarr's aide flies into a rage, claiming that it is all a Federation trick, prompting Klarr to finally get fed up and punch him unconscious. Klarr has his aide beamed back to his ship, and tells Kirk that he will be coming along with the Starfleet team to complete the mission. Everyone steps into the portal and disappears.
The Enterprise team and Klarr arrive in a strange place - a collection of large, solid square shapes floating in outer space. Spock quickly determines that this place is not actually real - it is a projection that uses the same holographic technology witnessed in Episode 2 ("Sentinels"). The massive face of a strange green alien with three eyes appears, and informs the team that they will now be required to answer a series of questions in order to earn the right to meet the Brassica.
The first question is "Who among you goes to the greatest pains in the pursuit of life?". The team is informed that only one of them may give the answer, and they are allowed to debate it before choosing. Kirk immediately offers himself as the answer, stating that a starship captain - seeking new life in the universe - goes through the greatest pains. Klarr counters this by pointing out that he is also a starship captain, and there is no reason why either he or Kirk would be the more "correct" answer. Spock offers himself, claiming that a Vulcan's pursuit of knowledge from birth to death may be the answer. McCoy argues that he - a doctor - is the answer. Finally, Uhura speaks up, pointing out that a female is the only possible answer, going through the pain of childbirth to bring new life to the world.
Confused, Kirk attempts to elicit hints from the Brassican face. When he does so, a different disembodied Brassican voice interjects in the conversation, mocking the humans and pointing out that asking for hints would be cheating. A third voice tries to defend the humans, pointing out that the differences between the Brassica and the humans may be making the test unduly difficult. Nevertheless, the Brassica give a cryptic hint that seems to indicate Uhura is the correct answer. Kirk allows her to present herself as the answer to the question, and she immediately disappears. The Brassica do not confirm whether this was the correct choice.
The next question posed is: "Who among you struggles most intently with the chaos of life?". Once again, Kirk offers himself as the answer, but Klarr points out that life on a Klingon ship is significantly more chaotic than on a Federation starship. Spock argues that a scientist's struggle to make sense of the chaos of the universe may be the answer. McCoy makes a more persuasive case: A doctor's struggles to keep his patients alive and improve the quality of their life. Once again, Kirk tries to question the Brassica for information about their philosophy and their wording, and points out the problem in asking philosophical questions of a different race that may not think the same way the Brassica do. Unfortunately, this only serves to intensify the argument between the different Brassica voices, and only elicits another cryptic hint. Nevertheless, Kirk finally chooses McCoy to give his answer, and he instantly disappears as happened to Uhura earlier.
The third question is much more complex: "Pig + X = Cow". When the remaining team-members begin to discuss this question, they quickly realize that each of them heard the question differently. Klarr heard something equivalent in Klingon to "Plant + X = Hive Paper", and Spock heard "Chicken + X = Reality". Klarr and Kirk both twist themselves into knots trying to find logical solutions to their questions, but can't even find a reason why the question they themselves heard is the correct one. Meanwhile, Spock concludes that the question itself is intentionally illogical, and determines that the answer is that there is no answer. After more arguing between Kirk, Klarr, and the Brassica, Spock is finally chosen to give his answer, and he too disappears.
In the last portion of the test, the Brassicans offer this ominous question: "Why should you be the one to leave this place alive?". Kirk and Klarr both realize that they are being pitted against each other, given that they are essentially enemies. Nevertheless, neither of them likes the idea of leaving the other one here to die. Eventually they decide to risk it, and tell the Brassica that they will either leave together or not leave at all. The Brassica appreciate the answer and congratulate Kirk and Klarr on their decision, inviting them to finally meet the Brassica face to face.
Kirk and Klarr are removed from the simulated testing grounds, to find themselves on a platform high above a Brassican city. The three Brassica previously heard arguing are here - plant-based creatures with four legs, three eyes, and green skin. The Brassica offer them formal diplomatic relations. The other members of the away-team also reappear, saying that the Brassica treated them well and had interesting philosophical discussions with them while they waited for Kirk and Klarr to finish the test. Spock reveals some more information about the Brassica - being a species that evolved from a plant and was often prey to other creatures, they have become isolationists who are wary of any other species. Tests seem to be a significant part of their culture.
While the teams wait for the Enterprise and the Klingon ship to arrive to pick them up, one of the Brassica (the one that was heard arguing against relations with the humans and Klingons) takes Kirk aside and tells him that the Brassica do not fully trust the Klingons. She produces an advanced data storage lense, claiming that it contains a scan of the entire Klingon territory, and asks Kirk to use it should the Klingons attempt to hurt the Brassica in the future.
Kirk takes the lense to Klarr and shows it to him. Klarr immediately produces another lense, saying that the Brassica gave it to him claiming that it contains a scan of Federation space. The Brassica warn the two captains not to destroy the lenses, pointing out that neither captain knows what is actually recorded on the lense they were given. Nevertheless, Kirk hands his lense to Klarr, pointing out that he is an honorable man and would destroy both lenses. Klarr does so, and the Brassica are overjoyed at this outcome, stating that this was the final test and they can now trust both the Federation and Klingon Empire. The humans and Klarr are transported back to their respective ships.
On the Enterprise, Uhura says the Brassica offered her the position of Ambassador, but she turned it down (partly for fear of this being just another Brassican test). Starfleet calls to congratulate Kirk on his success in opening relations with this new advanced alien race, and promising the Enterprise crew some shore-leave... sometime in the future.