The Enterprise has been joined by Admiral Justman and Ensign West, and they head off to Starbase 42, which orbits a planet rich in dilithium. They aim to get the Enterprise repaired there, but before much can be done, a Klingon warship (the D’k tahg with Koloth and Karel aboard) is identified as heading in their direction. Just before the Klingon vessel arrives, Klingon infiltrators disable the warp core on the station, and the warp core on the Enterprise had previously been powered down for maintenance. The Enterprise plays ‘dead’ after being attacked by the Klingon warship, while Scotty tries to get off the station and back to cold start the Enterprise’s warp core, and Spock is fighting his way to the engineering section of the station (through the invading Klingon forces) to cold start the station’s warp core. Meanwhile, Kirk is leading a group to protect or destroy the dilithium supplies on the station. During the battle, there are many casualties on the Federation side, including Admiral Justman, but the Klingons are defeated and another Klingon ship (claiming that the D’k tahg was acting without authorization) arrives to tow the D’k tahg back to Klingon space. However, towards the end of the battle, Kell and Karel come face-to-face, and Karel mortally wounds Kell before recognizing him. Before he dies, Kell passes his brother a data chip containing his views on the Klingons’ dishonor in the way they have been infiltrating the Federation, and when his body is recovered by the Enterprise, they finally realize that Klingons have been infiltrating them, and start to take measures to identify them.
The Enterprise is sent to the planet Nador to participate in the planet’s first true election, which is on whether to join the United Federation of Planets. Arriving at the planet, they observe that there is some opposition to the idea, and then the Enterprise is attacked by a small craft (which is easily driven off). When Kirk meets the ruling princes, Abon and Delor, he is surprised to find they are Siamese twins joined at the spinal cord. The first visit to the planet is marred by a riot of Federation civilians living on the planet and native Nadorians opposed to joining the Federation. The princes and other leading Nadorians are invited to visit the Enterprise but, while there, the Enterprise is hit in a missile attack and the princes are badly injured. In order to save them, Dr. McCoy has to separate the princes, and while the operation is successful, it leads to difficulties between the two who previously had to get on together. Not long afterwards, the Enterprise is attacked by a mysterious energy storm (certain parts of the planet are also attacked). It is discovered that the interaction of the psionic abilities of the separated princes is the cause of the energy storms, and that the two had actually been born separate, but joined to prevent such storms. McCoy comes up with a temporary method for combining their psionic manifestations and, when that fails, Spock creates a mindmeld between them, but that is also a short term solution. In the meantime, Kirk has tracked down two of the culprits behind the uprisings, namely two councilors, Hanor and Docos. Both councilors end up dead, one murdered by the other, who later commits suicide, but it is discovered that a third person is also involved. That turns out to be the wife of the Federation’s Commissioner Roget who was trying to smuggle out some of the planet’s statutory, to create additional funds for her and her husband. To solve the interaction problem of the two princes, Abon becomes sole ruler and Delor becomes the planet’s ambassador to the Federation. Kirk’s nephew Peter was on the planet and got into trouble, including getting captured. [Timeline: Stardate 3375.3]
Captain Garth has apparently been cured of his insanity, but now wants to return to Antos IV, the planet where he was cured after the transporter accident, but which he had then tried to destroy, claiming their shape-changing ability was too dangerous. The Antosians have always been a peaceable people, but Garth claims there is trouble brewing because some had got affected by his madness. Kirk is appointed to accompany Garth and keep an eye on him. On reaching Antos IV, Garth goes down to the planet first to meet with the planet's leader, Empynes, and a couple of days later Kirk and Spock beam down to join him and the group go with Empynes to meet the rebels. They meet with one group led by Heje-Illuss who were considering accepting Empynes's solution of having the shapeshifting ability removed, having seen how power hungry Hala-Jyusa (the leader of the other rebel group) had become. Then the group finds themselves surrounded by Hala-Jyusa’s rebels and see that Garth is leading them (the person they had thought was Garth, while travelling with Empynes, was actually a shapeshifting rebel). Scotty saves the day by beaming the Enterprise team and Garth up, and Garth then claims that he had infiltrated the rebel group to try to convert them from inside. The rebels get transported to another island, but they morph into birds and try to fly across the ocean. Hala-Jyusa and others die in the attempt (the Enterprise crew is able to save a lot of them). Empynes finally decides to drop his plan to have the shapeshifting ability removed from the population, and agrees that they will somehow have to learn to control it. Regular contact with the Federation is established and Garth is appointed ambassador to the Antosians.
The Excelsior is on a mission to negotiate with the Tholians, but a breakdown in negotiations occurs when the Tholians discover (thanks to being told about it by the Federation ambassador, Burgess) that Captain Sulu has sent out probes to investigate a dispute that seems to be occurring on the far side of Tholian space. The Tholian ambassador, Kasrene, is killed by another Tholian to prevent him telling the Excelsior team about the dispute. Sulu orders the Excelsior to go and investigate, keeping close to the interspacial rift to mask their passage as much as possible. They arrive in the region of the dispute and find a ship attacking a Tholian colony. They intervene and disable the attacking ship, recovering the body of one of the aliens, who later surprises them by recovering. Actually, the alien had already surprised them by having DNA that matches human DNA, although the alien looks remarkably un-human, with tough skin, opposable thumbs on his feet, and a tail. At this point, a fleet of Tholian ships arrive and accuses the Excelsior crew of being in league with the attacking aliens. It turns out that the aliens, who call themselves the Neyel, are the descendants of the inhabitants of Vanguard, an O’Niell colony that had got blasted 200 light years into deep space when an experiment to form a toroidal subspace warp field went wrong. It had then fallen through the rift near Tholian space and ended up in the small Magellanic cluster. They had become very warlike and untrusting of other aliens after their initial encounter with aliens had resulted in their original director being beheaded. They had traveled through the rift trying to find a way back to Earth and had attacked the Tholians, who had retaliated and tried to close the rift, resulting in danger to the Neyel’s current homeworld. Both sides of the dispute considered the other side non-sentient and only worthy of extermination. The Excelsior crew had worked out a way to escape from the Tholian web surrounding them, but Sulu wants to find a way to bring the dispute to a peaceful end and challenges the Tholian captain, Yilskene, to a TruthCombat. Before that happens though, the Excelsior and the Neyel ship escape through the rift and visit the Neyel homeworld, but they return in time for the TruthCombat, which the Tholians see as a fight to the death. Ambassador Burgess and Tuvok do not seriously expect Sulu to win the swordfight using Tholian monoblades and they decide to take their own action. Aided by Lojur (who had lost his fiancé in the battle with the Neyel), Burgess and Tuvok take the ambassador’s shuttlecraft and abduct the leader of the Neyel ship, Jerdahn, and beam off the Tholian captain along with Sulu, just after Sulu had actually disarmed the Tholian in combat. Sulu is unhappy about the abduction. When the Tholians and the Neyel get talking to each other, they do come to a peaceful settlement, although it means closing the rift which cuts the Neyel off from relatively easy access to Earth. Before the rift closes, Burgess flies her shuttle through it, aiming to dedicating her life to readying the Neyel for eventual contact with Earth. [Dateline: year 2298, 5 years after the Khitomer Accords]
Peace negotiations are going on between the Federation, the Klingons, and the Romulans (who have been annexing planetary systems recently). The Enterprise-B, captained by John Harriman, with Demora Sulu as his First Officer, is sent to the Bonneville Flats to witness the trial flight of the starship Universe, using a new hyperwarp drive. The Universe explodes soon after achieving hyperwarp, and Admiral Harriman (John Harriman’s father) is badly injured when the ship he was on, the Ad Astra, is caught in the blast, and he later dies. A cloaked Romulan warbird observes the explosion and concludes that it was a test of a metaweapon, and throws the peace negotiations into turmoil. The Federation sends the Enterprise to Space Station Algeron, in Romulan space, to deliver the records of the flight and the specification of the failed hyperdrive to both the Romulans and the Klingons. John Harriman still suspects that Admiral Vokar, commanding the Romulan flagship, Tomed, is intent on starting a war with the Federation and when the Enterprise leaves Romulan space he stays behind on Algeron. He had made a comment to Sulu that got her checking up and discovered that people, who she knew had died, had apparently been later assigned to different starships, and she suspects that they are Romulan spies and reports it to Admiral Mentir. He confirms that there has been one aboard Enterprise, who is then taken into custody, but the other mystery people are related to something else. A little while later, the Romulan flagship, Tomed, emerges from the Neutral Zone at high warp and explodes, destroying the Foxtrot Sector along with apparently four thousand inhabitants. As a result of the measured response by both the Federation and the Klingons, the Romulans do end up signing a treaty, but only to keep within the bounds of the Neutral Zone (but at least war is prevented). In actuality, the Foxtrot Sector had been vacated of all inhabitants and replaced by equipment to simulate biosigns, and the Universe had been unmanned and using a version of the known defective transwarp technology. The Tomed had been taken over by a team consisting of John Harriman, Elias Vaughn and Commander Gravenor, after most of the crew had evacuated the ship when the team created a malfunction in the containment of the singularity used to power the warp drive. Romulan Admiral Vokar had suspected a Federation plot and had stayed aboard with five others, but all six Romulans died either trying to stop the team or in the resulting explosion. After the mission, John Harriman resigns his position aboard Enterprise and Demora Sulu becomes the new captain. Chancellor Azetbur is assassinated on the orders of General Kaarg. [Dateline: year 2311, 18 years after Kirk’s supposed death aboard Enterprise-B]
Gul Monor of the Cardassian ship, Sontok, discovers a planet, Raknal V, rich in zenite, but they also find an ancient crashed spaceship. A cloaked Klingon vessel, the Wo’bortas, captained by Qaolin, has been following the Cardassians and realizes that the wreckage is that of the Ch’gran colony ship, the first Klingon vessel to venture out after the Klingon homeworld was attacked by the alien creatures. A battle ensues between the Klingons and the Cardassians but a stalemate emerges and the Federation is called in to negotiate a settlement, led by Ambassador Curzon Dax and also including Elias Vaughn. Dax ends up with a settlement whereby both sides will attempt to colonize a continent on the planet and the more successful of the two will keep the planet. This drags on for years, with growing tensions between both sides, and real and suspected sabotage and attacks from both sides. It also leads to the Romulans taking advantage of the tensions to carry out attacks of their own. As a result of one piece of sabotage, Ian Troi (Deanna’s father) dies. The issue is only resolved when Kravokh, the chancellor of the Klingon Empire (who had been adamant about regaining the Ch’gran wreckage), dies and the Klingons concede ownership of the planet to the Cardassians and start negotiations for the Ch’gran wreckage. It is then revealed that Kravokh had been protecting the memory of Ch’gran because Ch’gran had intended to return and take over the Klingon homeworld as the new emperor, but his crew had mutinied and continued his supposed original exploration mission.
Rachel Garrett is captain of the Enterprise-C, and her new second-in-command, Halak, takes a shore leave to the planet Farius Prime to follow up on a request from the lady (Dalal) that had largely raised him after his parents died. Halak is concerned about Arava, an old friend and ‘almost a sister’, who is involved with a criminal gang, Asfar Qatala. Unfortunately, Halak’s lover aboard Enterprise, Batra, follows him. When things go wrong, Batra manages to save Halak’s life but gets killed herself. Back aboard the Enterprise, an enquiry is held and Special Agent Laura Burke from Starfleet Intelligence arrives, accuses Halak of being involved with the Orion Syndicate, takes him into custody and removes him from the Enterprise. Meanwhile, Garratt has had a call from her ex-husband, Kaldarren, and her son, Jase, who are on their way to some archaeological site, supposedly to locate a portal that the Hibitians (a race that the Cardassians claim to be descended from) used to travel from planet to planet without spaceships. Kaldarren doesn’t realize that the person organizing the trip works for the Asfar Qatala and intends to take the plans of the portal (if found) and any treasure and kill anyone in the way. It also turns out that Laura Burke’s real name is Talma Pren and she is really an assistant to the leader of the Asfar Qatala, but is now out to make her own fortune from the supposed discovery of the portal, and is using Halak’s knowledge of the Cardassians to acquire the portal information for herself. Also, Dr. Stern had secretly implanted a transponder in Halak, before he was taken from the Enterprise, so they are able to track his whereabouts. Kaldarren’s group arrives first at the planet where the portal is supposed to be, during a time they know the Cardassians will not be present, and they finally discover there is no portal. However, there is an underground cave system in which are trapped the disembodied spirits of Immortal Uramtali, the dithparu, who had been using the kings of the now extinct race that used to live on the planet surface to escape their captivity one-by-one. These spirits use Garrett’s son and the son of the ship’s captain to lead Kaldarren to them. When Kaldarren realizes that others will be taken over by these malicious spirits, he offers himself and is able to contain them but ends up dying. Meanwhile, Talma has brought her ship to the planet and sent Halak and an associate down to locate the portal (following the biosigns of those already in the caves), and then the Enterprise arrives and Garrett also takes a shuttle down and rescues her son and Halak. By this time the Cardassian patrol ship has returned and starts firing on the Enterprise, and Garrett doesn’t want to start an incident with the Cardassians by directly firing on their ship. Instead, she sets of an explosion that ignites the plasma in the system and causes the star to explode, vaporizing the system, and the Enterprise is the only ship to escape from it. Halak is cleared of all charges and reinstated as second in command of the Enterprise.
Uhura is head of Starfleet Intelligence and contemplating retirement. Then her contact in the Romulan Senate, Cretak, sends a young orphaned girl, Zetha, to her with a message about a possibly manufactured disease that is 100% fatal to those that get it, and which is affecting a number of Romulan planets and has spread through the neutral zone to Federation territory. Uhura organizes a mission aboard a converted freighter (that becomes known as the Albatross) captained by Benjamin Sisko, and with Tuvok, Dr. Selar, and Zetha aboard. Uhura, Dr. Crusher and retired Admiral McCoy join them via an experimental holotech system. They discover that the disease, a combination of Gnawing (an historic Romulan disease) and Rigelian fever, was developed by the Rigelian named Thamnos, who was using the name Cinchona and living on the planet Renaga in the Neutral Zone. He knew that something, known as hilopon, in the planet’s soil would cure that disease and many others, and he wanted to be the hero by providing the cure. Unfortunately, he didn’t realize that hilopon would not work anywhere but on that planet. Also, Koval, of the Romulan Tal Shiar, effectively took over the plan for his own reasons and infected thousands more than Thamnos had intended doing. He had created a number of carriers to spread the disease (which became known as Catalyst in the Federation, before being officially denied), and Zetha was unknowingly one of them, but she and some others actually proved to be immune to it and became a source for a vaccine. The Albatross team locate Thamnos, but he gets killed by his Renegan wife, and Sisko and the others get rescued by the starship Okinawa (with Admiral Curzon Dax aboard) after a showdown with the Romulan warbird captained by Admiral Tal. [Timeline: year 2360, 67 years after Kirk’s supposed death aboard the Enterprise-B, 4 years before the launch of the Enterprise-D]
The Enterprise is called upon to transport San Cogley and his associates, Areel Shaw and Judge Manuel Carabatsos, to the mining colony on Aneher II where Administrator Daniel Latham has been found murdered. The Klingon Commander Mak’Tor has been arrested after being found kneeling alongside Latham’s body with Latham’s phaser (the murder weapon) close at hand. Areel Shaw is prosecuting the case, and looking forward to winning after having lost to Cogley when he defended Kirk. It is discovered that a file had been deleted from Latham’s computer shortly before Latham’s body was discovered, and when the file is recovered it is found to be a report to Starfleet, including mention of the Klingons smuggling replacement miners onto the planet (the Federation and the Klingons are trying to establish their respective rights to colonize the planet, under the Organian treaty). The report seems to cast more evidence against Mak’Tor, but Cogley starts to wonder why Latham’s body and the computer weren’t vaporized if Mak’Tor really had committed the crime. Cogley discovers that Latham had had a serious dispute with his wife, Helen, shortly before the murder, and that a number of people had possible motives for murdering him. During the investigation, one of the miners is uncovered as spying for the Klingons, but Cogley finally exposes Latham’s second-in-command, Grig Nemov (who is also Helen’s lover), as the murderer, after finding Latham’s original hand-written draft for the file that had been deleted from the computer. Latham had been suggesting that the whole of the senior staff should be replaced, and Nemov had expected to lose out on the profits he was hoping to achieve. [Timeline: 2267, circa Stardate 4521.7, soon after the incident at Mudd’s planet]
Soon after their encounter with V’Ger, the Enterprise is sent to try to help resolve the growing troubles on Daran IV, where the inhabitants of the Fabrini worldship, Yonada, have settled. The former high-priestess, Natira, has been trying to lead the population on a secular path (following the example of the Vulcan head of the Federation team there, Soreth). Dovraku is leading a kind of holy war to restore the position of the Oracle, and in fact wants to ‘merge’ with the Oracle, just as Decker had merged with V’Ger. In the middle-ground is Rishala, who has been appointed as the new high priestess, and is not really trusted by the other two leaders. Kirk convinces Natira that negotiations with the people of opposing views is the only way to bring peace among the population, and a meeting on Yonada (now in orbit of Daran IV) is arranged between Natira and Rishala and other leaders, although Dovraku is not willing to be part of the negotiations. He does, however, smuggle supporters into the meeting who take the place over and he tries to get Spock to act as the intermediary in the proposed ‘merging’ of him and the Oracle, by having Spock mindmeld with the two. However, during the meld Spock is able to bring to the fore the incidents in Dovraku’s past that had caused him to act the way he had been doing and Dovraku is unable to handle the revelation, and as a result is no longer a problem. During the investigation, many things about the Fabrini and Yonada history are uncovered, and the remaining leaders plan to work together to try to accommodate the differing viewpoints that people have. The other inhabitants of the planetary system, the Shesshran, caused some interference, but nothing that Sulu couldn’t handle. [Timeline: Stardate 7438.7]