A distress call had been received from the Horatius system that is well outside normal Federation territory, and which has three Earth-like planets that have been colonized by different groups of humans over time. The Enterprise is sent to investigate, even though it is running low on supplies and Dr. McCoy is concerned about the crew and the potential for cafard (space sickness). When they finally reach the system, they initially check out the planet Neolithia which was settled by people reminiscent of the Native Americans who wanted to live without technology. Kirk and the others in the landing party get accused of being associated with raiding parties from space that had been abducting clan members, and the team is sentenced to death but they escape and get themselves beamed back to the ship. The young warrior (Grang of the Wolf clan) who led them to the tribal leaders is also condemned, but he hides in the specimen container that the team had taken to the planet and is beamed up with it. The Enterprise then goes to the planet Mythra, which proves to be a theocracy where the priests keep the general population under control using a hallucinogen (called anodyne and similar to LSD) in the drinking supply. That planet had also been affected by the space raiders. McCoy comes up with an antidote to the hallucinogen which gets beamed into the main city’s reservoir, expecting that the few pseudo-priests will not be able to retain their position when the population gets their senses back. The inhabitants of the third planet, Bavarya, have a Nazi-style leadership that (under pressure) admits to plans for taking over the other two planets and ultimately the Federation. Kirk and the landing team (which includes Grang, who identifies the Bavaryans as being the raiders) are taken prisoner and are brought to the palace arena to face three of their champions in a televised duel. The planet’s leader, Nummer Ein, has a daughter, Anna Shickle, and she lets Kirk know that she was the one who sent the message for help. During a recess in the gladiatorial-style duel she frees the team and explains that the population consists of Herr-Elite and Doppelgangers, the latter being multiple zombie-like duplicates of the best of the soldiers. She also explains that her real father is dead, and that Nummer Ein is a Doppelganger copy of him. Then she leads them to the duplicating banks, the machinery that produces and sustains the Doppelgangers. Nummer Ein bursts in, but blows himself up when he discards Spock’s warning about the phaser he is using being set to overload. Then the team turns off all the Doppelgangers (who just disappear, presumably having some holographic aspect to them) and then they destroy the equipment that makes them (and which the Herr-Elite knew how to maintain but not reproduce). Anna says she will work with others to establish a better society. Grang gets returned to his people, where he is given a hero’s welcome after Kirk gives a slightly exaggerated story of how Grang stopped the raiders. On the three month journey home, a rat that Sulu had purchased (named Mickey) causes chaos on the ship when it supposedly escapes and is believed to be carrying the Bubonic Plague, but it was all a ploy by McCoy and Spock to provide some excitement onboard to counter the space sickness. [Timeline: Stardate 3475.3]
The Enterprise is benchmarking in an arm of the galaxy on the far side of Klingon territory when word comes through that the Klingons have launched an offensive against the Federation, and the Organians (who would have been expected to intervene) seemed to have vanished. The Enterprise finds itself effectively cut off behind enemy lines, and Kirk opts to head for Organia to find out what has happened there. It will take several months to get there, with a lot of that time being within Klingon territory, so they maintain a communications blackout. Scotty and Spock come up with a way to find out what had happened to the Organians sooner, by adapting a transporter to make a copy of Spock using tachyons (which can only travel faster than light and have no known upper speed limit). The idea is for the copy to go to Organia and return after one day to pass on the information before reverting to tachyons. However, when they try it, the result is two Spocks on the transporter platform, both claiming to be the original with neither apparently having visited Organia. Kirk starts referring to them as Spock One and Spock Two, and initially tries to share Spock’s duties between them, but then it is found that one of them had caused the Enterprise to drop out of warp temporarily, possibly revealing the ship to the Klingons, so Kirk has both of them confined to quarters. Then Spock One barricades himself in McCoy’s laboratory and refuses to come out unless Spock Two is killed (Spock Two expresses similar feelings about Spock One). When the Enterprise gets to Organia, it finds the planet surrounded by an energy field that causes intense mental anguish when they approach it too closely. They also discover a fleet of six Klingon ships there, but they succeed in destroying them. After studying test animals sent through the same transporter, McCoy realizes that the duplicate Spock would be a full mirror image of the original, and would be unable to survive on standard food that uses ‘left-handed’ amino acids. That shows that Spock One had to be the duplicate (he had been using McCoy’s lab equipment to remake his food). Kirk orders that McCoy’s laboratory be broken into and Spock One arrested, but he had escaped through the ventilation ducts and later steals a shuttle (that he had converted to be warp capable) and heads for Organia. It is established that the energy field had been the reflector that had caused the duplication of Spock, but Kirk, Spock Two, and Scotty are able to use a regular transporter to beam down to try to disable the field that the Klingons had established to confine the Organians. Unfortunately, Spock One was already on the planet and a battle of minds ensues, resulting in Spock One being killed when he believes he is thrown into the energy barrier. By this time a Klingon fleet had arrived, and, following Kirk’s orders, the Enterprise was attempting an escape. Kirk, Spock and Scotty now meet with the Organians, and using equipment that Scotty had brought with him, plus equipment from the shuttle that Spock One had stolen, Scotty is able to counteract the energy field, freeing the Organians who quickly bring the war to an end. [Timeline: Stardate 4011.9 through 4205.5]
The Enterprise is studying the humanoid inhabitants of a pre-warp society on the planet Kyros, where most of the inhabitants keep their heads covered. The Enterprise is testing a new telescan implant system that links the minds of the members of the study team with individuals (referred to as ‘dops’ or doppelgangers) among the native inhabitants. That lets the team members have access to the language and culture, plus the abilities of the dops. The system is, of course, meant to act one way. The very reserved Ensign Sara George is in charge of the implementation of the system, and she decides it might be fun to select a very promiscuous belly dancer as her dop, but the influence from her dop leads Sara to pick a randy individual for Spock (who she is infatuated with). Unfortunately, the hillman, Chag Gara, selected for Spock was of low intelligence and considered himself a messiah, although he hadn’t drawn much of a following. However, it seems that Spock inherited the messianic drive, and aided by his logic and intelligence, his success blossoms. As Messiah, he plans to make use of the Enterprise, so he first disables the warp drive to prevent them leaving, but he is unaware that a radiation front, that could irreparably irradiate the Enterprise, is approaching. A number of attempts to kidnap Spock or Gara, with the aim of breaking the link between them, fail. Then they come up with a nullifer that can break the link if they can get it close enough to Spock, and the only way they see of doing that is to use the seductive powers that Sara has inherited to get Spock’s attention. By this time, the Messiah has gathered the hill clans and is moving to attack the main city, Andros, so Kirk and his group (including Sara) join the assembly. The seduction works, but the Messiah realizes who is involved and Kirk’s team, minus Sara but including the local chief (Tram Bir) that Kirk’s team had teamed up with, get captured and staked out ready to become a burned offering come sunrise. When Sara gets the Messiah undressed in the dark, she finds he doesn’t have pointed ears, so must be Gara. Apparently, the link had worked both ways and Gara had been able to control Spock, keeping him in a catatonic state but with Gara able to use Spock’s abilities. Sara is able to knock out Gara and get the nullifier close enough to Spock to break the link. Spock saves Kirk and the others and does one performance as the voice of the gods to tell the hill clans to return home and live in peace. Gara gets taken aboard the Enterprise so that McCoy can alter his memory and remove his messianic tendency. [Timeline: Stardate 6720.8]
Omni is an over-sized human-shaped person with Vulcanoid strength who has established a planet where people are supposedly free to do what they want, although he has Romulan guards protecting himself. The planet appears to be modelled after the old Wild West of the United States. He has assembled a group of delegates, and the Enterprise is sent to represent the Federation. They find three Romulan ships in orbit, headed by the female Fleet Commander that Kirk and Spock had stolen the cloaking device from. Despite that, she seems to still be infatuated with Kirk and Spock, and while Omni appears to have some backing from the Romulans, the Commander is suspicious of him. On a tour of the planet, organized by Omni, they see a lady (in accordance with the customs of her community) try to immolate herself and her child by running into a burning building. Kirk intervenes and saves the baby, but the building collapses from the fire, killing Kirk and the woman. Omni says Kirk’s attempted intervention shows what a farce the Federation’s Prime Directive is. Kirk’s remains are returned to the Enterprise and McCoy confirms they are Kirk’s, but Spock is sure the event was staged by Omni and was a clever murder. He and the Commander go to confront Omni, who produces a living copy of Kirk and says Spock can have him if he will condemn the Federation to the delegates, and then Spock and the Kirk-copy (who becomes known as James) will have to join the Commander and go to the Romulan Empire. Spock does a mind-link with James and establishes that he is a real duplicate, and initially agrees to Omni’s terms. Then the Commander and James see a screen showing that the original Kirk is still alive and being held captive by Omni. Omni had beamed Kirk out from the building as it collapsed, simultaneously beaming in an unfinished copy that provided the remains, and then went on to use the recording from the beam-out to create the living copy (James). Omni planned to keep the original (Jim), but James feels a psychic link to him (that grows when Jim suffers the pain of a thorough beating from Omni). James and the Commander start tracking him down, and Spock (who had been on his way to address the delegates) uses his link to James to follow them. The fight with Omni swings back and forth, but Omni escapes from Spock’s grip and a mindmeld by shooting himself, knowing that he has set up the mechanism to resurrect himself, although the process is not instantaneous. Jim, James, Spock and the Commander beam themselves up to the Enterprise and discuss what to do with the planet. They appear to have spent too much time talking, because Omni suddenly appears among them, but Kirk had concealed a gun on himself and, as Scotty beams Omni’s phaser away, uses the gun to kill Omni. The hope is that Omni will be too far from his resurrection machinery and will be truly dead, although he had triggered the transportation of his body as he died. James (who gets transformed by McCoy to look like a Romulan) decides to go with the Commander as her noble tribute-liege, leaving the original Kirk (Jim) as captain of the Enterprise.
Black Omne, also known as Omnecron, finds himself resurrected after Kirk had shot him. The Romulan female Commander takes James (Kirk's duplicate, now disguised as Romulan). Kirk worries about a Spock duplicate. Omne reappears as Regent at the Voran Dynasty Hegemony Conference, trying to pull the group out of the Federation, but saves Spock and Kirk when the conference is attacked by Omne's duplicate in the shape of Spock. The Commander takes the Doyen of Thorva's prince as tribute, planning to substitute James and return the prince later. The prince gets abducted by Omne/Spock and James gives chase, with Jim Kirk and Omne also after him. They end up on a planet protected by a vortex (making approach almost impossible). The planet is Omne's base, and the Vortex is also a path to another universe. Omne/Spock gets really killed, Omne gets marooned on the planet in the other universe, but James gets drawn back there as well, just as he is about to truly commit to the Commander, and the vortex closes for 53.725 years.
The Enterprise discovers an Earth-size and Earth-like rouge planet, not orbiting a star, but with its own small star-like object in orbit about it. They call it Anomaly, because, although it has obvious artificial features and has plenty of lifeforms, sensors do not identify any intelligent life. Finding they cannot beam down, Kirk heads an away team that takes a shuttle down to investigate the planet, but, when they land, the shuttle becomes mainly inoperable and they are unable to contact the Enterprise. On the Enterprise, they can see where the shuttle landed but they are unable to pick up life-signs or other indication of the crew. Spock sends another shuttle on a rescue mission, but that gets stranded along with the first. After being unable to contact either team, Spock leads a further three shuttles with supplies for a long-duration stay, and leaves orders for the Enterprise (which was unable to send subspace messages due to some effect from the planet) to continue to its original destination (Starfleet Academy on Earth) and get help. On the planet, it is found that there are plenty of dangerous creatures around, and while the team’s phasers work on stun, no higher settings are operable. They lose one crew member to a carnivorous plant, and one to an attack by primates with no eyes, ears or mouths. Another of the team (Hixon) is injured and then wanders off the following night and comes back, seemingly happy but partially changed into one of the native primates, and that change continues. There is a sentient race on the planet, who use the term Arivne to describe themselves, and who don’t need eyes, mouths, etc., because they connect directly with the energy/matter/thought (which they see as one) of the universe directly. The primates are immature versions of them. The Arivne say they want to experiment on some of the Enterprise team (Spock, McCoy and a group of scientists including Dr. Atheling who the Enterprise had been taking to the Academy). They send Kirk and the others (including the shuttlecraft) directly back aboard the Enterprise. The Arivne claim they need to find out about things like problem solving and deceit, because a powerful but violent association of races (the Irapina) have contacted them. The Irapina are from the Sagittarius arm of the galaxy, but are planning on conquering the Alpha Quadrant. The Arivne seem to learn quickly about deceit because they have played with the Enterprise’s computer, making it send out a fake warning about the crew having been infected by a virus with psychic and physical symptoms that is making them delusional, and the U.S.S. Lysander arrives to quarantine the Enterprise. However, the Arivne then decide they need Kirk, so they get the Enterprise to head back to Anomaly, although they whisk Kirk off the ship and back to the planet first. That was because they had exaggerated the abilities of the Federation members to the Irapina, and the Irapina were sending three ‘champions’ ahead to challenge representatives of the Federation (Kirk, Spock and McCoy) to see what the competition is like. The Arivne secretly assist the Federation group, and they are doing well, but then Spock sacrifices himself to save Kirk (which the Irapina see that as underhanded) and Kirk wards off a final attack, visualizing the Irapina as ants. The Irapina decide to head towards Romulan space instead. The Enterprise team are returned to their ship (minus Hixon who is now an Arivne) and the Arivne wipe their location from the Enterprise’s computer to maintain their anonymity. Once it’s over, the Enterprise crew speculate on whether the Irapina are real or just another test by the Arivne. [Timeline: circa Stardate 6132.8]
A report is being prepared for the SAB (Scientific Advisory Board) about Mudd’s adventures, but the Enterprise command crew feel it doesn’t capture the flavor of events, so Lawrence, the Integrator, is given the job of preparing a second, more compelling version.
The first two sections of the book retell the events depicted in the Mudd’s Women (Stardate 1329.1) and I, Mudd (Stardate 4513.3) TV episodes.
The third and final section is titled The Business, As Usual, During Altercations. The Federation planets (and it is soon learned, the Klingons and Romulans) are experiencing a shortage of dilithium crystals, handicapping their spaceflight capabilities, and the Enterprise is sent to find out why. They find that the various mining colonies had all made deals with a fat, jovial, salesman to sell their dilithium to him in exchange for beautiful wives (which McCoy ascertains are not human). The companies making these deals all appear to be based on the planet Liticia, which turns out to be the same as Mudd’s Planet. Mudd had smooth-talked the androids on the planet into accepting him as their ruler again, and had converted the Stella androids into spaceships and used them to set up the dilithium contracts. When Kirk confronts him, Mudd escapes aboard the Superstella with all the dilithium crystals, and tries to auction the supply off. However, the Enterprise track him down and the Superstella escapes towards the galaxy barrier with the Enterprise on its tail. Crashing through the galaxy barrier results in them being thrown into the Small Magellanic Cloud, and it is found that the contact with the barrier was now causing the dilithium crystals to grow. The Enterprise has to jettison its supply and then rescue Mudd and his androids as their dilithium horde grows and breaks up the Superstella. With the ship’s energy fading and the growing dilithium mountain starting to destabilize stars, it looks like the end, but the exploding stars blast the Enterprise back through the barrier into the Milky Way galaxy. They also get sent back in time to when Mudd had been making his first deals with the miners, and the Federation hadn’t noticed any dilithium shortage. Consequently, no one takes Kirk seriously to start with, but once they start to check, they find that it does make sense, and Kirk is given free reign regarding Mudd. First, Kirk tries returning him to the real Stella, but she and her mother make it very clear they don’t want him. Returning to Liticia/Mudd’s Planet, the androids have declared themselves an independent sovereign planet, applied for Federation membership, and put Mudd on trial. The only thing they find they can really convict him of is commanding a ship without a license although they do determine that he is a menace to the galaxy. The sentence is banishment from the Milky Way galaxy aboard a specially built craft, an improved version of the Superstella that can survive the Barrier, and with a non-sentient robotic crew. Kirk speculates on whether Mudd will also blow up the Large Magellanic Cloud or sell it. [Timeline: Stardates 6273.6 – 6063.5]
The boundaries of the Romulan Neutral Zone are determined by the strength of the magnetic field, and ion storms are changing those boundaries and the planet Arachnae will soon move into Romulan space. The Federation Council sends the Enterprise to ascertain if the man-sized spider-like Arachnians are sentient or not, and if so, convince them that they should become Federation members. Dr. Katalya Tremain, a noted biologist admired by both McCoy and Spock, is assigned to the mission, although Kirk is warned ahead of time that she can be ‘difficult’. That turns out to be because she hates all Vulcans, and when she finds that Spock is aboard and will be working with her, she refuses to go until directly ordered to. McCoy and Spock find that her husband (Jeremy Tremain) and her parents had died aboard the Federation ship Calypso after it had been infected by parasitical creatures that were causing the ship to disintegrate and would kill them all. Captain Selik, a Vulcan, had ordered the Calypso blown up by lowering the shields between the drive’s matter and antimatter. By the time the Enterprise reached Arachnae there is only about 36 hours left before the planet moves fully into Romulan territory, and the team beams down (under protest from Katalya) to begin investigations. Soon after setting up camp, while Spock and Katalya are investigating a cave, the Arachnians emerge from a concealed underground system and attack the others at the base camp, killing eight of them and leaving the other two seriously injured. The injured two die soon after because a Romulan ship, the Decius, had arrived and Kirk felt he couldn’t afford to lower shields in order to beam the survivors up. Under the circumstances, Spock (who suspects the Arachnians are sentient) and Katalya (who believes they aren’t) decide to try to complete their mission. Finding their way carefully through the tunnels, they observe an ornate cave ‘city’ of the Arachnians, which does nothing to change either’s view. On their way out of the tunnels they are attacked by a group of Arachnians and Spock gets injured. The Arachnian bite can lead to a very painful death. Spock, who is unable to move much, gets Katalya to return to their cave shelter to get some supplies, then he drags himself back into the tunnels, finds and stuns a lone Arachnian and mindmelds with it in an attempt to prove that it is sentient. Unfortunately, he proves that it isn’t, and his own mind is affected by the contact, and he starts to believe he is an Arachnian. To save him, Katalya mindmelds with Spock and it gets revealed that Katalya’s marriage to Jeremy had been effectively over (as she had said) and that she had fallen in love with Selik. She blamed herself for the deaths of those aboard the Calypso because she could have been there and might have changed things, and she took to hating all Vulcans to hide from herself the fact that she loved Selik. Katalya now has to come to terms with the reality of the situation. The mindmeld also reveals what Spock had discovered about the Arachnians being non-sentient, so Kirk feels free to concede the planet to the Romulans and tells them he is dropping shields in order to beam Spock and Katalya up. Then they leave the Romulans to enjoy their encounter with the Arachnians, and Katalya is considering living on Vulcan for a time, as part of her recovery process. [Timeline: Stardate 6451.3]
The Enterprise is on a mission near the Galactic Core when it gets drawn into a Dyson sphere (a hollow artificial planet with a small star in the center). The inhabitants (known as Lyrans) are a race looking like white furred chimpanzees who consider the sun to be a god called Ay-nab. Events lead the Enterprise crew to believe there may be some truth in the belief, and they find a number of other spacefarers who have been captured in the Dyson sphere, and on whom Ay-nab apparently “feeds”. Among these spacefarers are Uhura’s father, one of Kirk’s academy roommates (Thomas Clayton), and the crew of another Starship vessel. They also find a Klingon ship that has been recently caught in the sphere, and who apparently want to cooperate with Kirk and his crew (but who Kirk does not fully trust). Then it is discovered that the sphere is heading towards a black hole, and consequently faces destruction. One of the Lyrans, Ola (whose life Kirk had saved), shows Kirk how to contact Ay-nab, and he convinces the star/god (or whatever it is - Spock prefers to think it might be a computer) to let then go. The Klingons also get their freedom, and Ola escapes with the Enterprise. After the Dyson sphere has entered the black hole, Spock gets a telepathic message, apparently from Ay-nab, saying that it and its children are well. [Timeline: Stardate 6527.5.]
The Enterprise is returning Captain Kostas Spyroukis and his daughter, Metika, to their colony world (Delta Epsilon 4) after a failed attempt at getting the colony accepted as a full Federation member planet, instead of just a colony. Spyroukis falls seriously ill and dies soon after boarding the Enterprise. It is found that the zeton radiation from the system’s star had affected the argon gas in the colony’s atmosphere and given him argon poisoning. It is discovered that Metika and, presumably, all the colonists are also suffering from the same ailment. Spyroukis had initially discovered the planet, so he had three month’s more exposure that the others. The Enterprise is assigned to evacuate the colonists and, to save time getting to the colony, Kirk orders the ship to travel through an extreme nebulous region, classified as a Class Two hazard. The ship gets swallowed by a rift in the fabric of space, and then find that there are also a Klingon and a Romulan ship in the bubble of space they find themselves in. A little gnome-like creature appears, who calls himself Enowil and says he is an Organian but had fallen out with the other Organians. He sets the command crews of the three ships a puzzle, to work out what it is that he is missing from the bubble of unreality he has built for himself, and he offers the winner a prize of whatever they desire. When Kirk explains the mercy mission they are on, Enowil says they are free to leave any time and he will even drop them off at the colony’s planet, but Kirk is wary of what the Klingons or Romulans might ask for if they won, so he says the Enterprise will stay for at least a few days. Enowil takes the three groups on a conducted tour of the world he has created, but every time someone suggests something that he might be missing, he is able to show that he already has that. Then the Klingon captain, Captain Kolvor, talks Metika (who is getting frustrated by the delay in evacuating the colony) into planting a bomb on the Romulan ship. She is discovered and stopped by Marcus Claudius Breccio, although the two then find themselves in a back-of-house area on Enowil’s world. After finding their way along a seemingly endless wall, saving each other from various mythical-like creatures along the way, they finally locate a door. Going through it, they find themselves in an arena where the three teams have been watching a gladiatorial-type display. After what they have gone through together, Breccio tries to cover up Metika’s involvement in the attempted bombing, but seeing that he is getting himself in trouble, Metika admits her guilt. Kolvor then has himself beamed aboard the Enterprise with another bomb, but Kirk stops him, although Enowil had obviously been tracking events and prevents anyone fatally injuring any of his ‘guests’. McCoy had noticed how Enowil was interested in what the three groups had been doing, and had been happy when people had expressed delight in any of his creations and disappointment when they didn’t want to see everything he was doing. So, he suggests that what Enowil needs is an audience. Enowil immediately creates an audience but Kirk points out that they are his own creation and predictable, not unpredictable real people. Enowil finally agrees that that is what he was missing, and says the prize goes to the Federation team. Kirk says the prize he would like is for the colonists to be cured of their radon poisoning and a new planet be created for them that will be called Spyroukis. He says the colonists should be free to visit and vacation at Enowil’s world, and be free to come and go as they will. Enowil also offers Metika and Breccio a home, since both of them would be in series trouble if they returned to their own homeworld. Enowil had already sent the Klingon ship (the Destructor) back to their domain, and he now does the same for the Romulan ship (the Talon, captained by Commander Actius Probicol), and drops the Enterprise off at the colony. [Timeline: Stardate 6188.4]
The Enterprise discovers a giant interstellar craft, like a hollowed out asteroid powered by a Bussard ramjet, which appears to be off-course. When an away team, headed by Kirk, transports into the craft, they find that the immensely dense skin doesn’t allow them to transport back. Shortly after discovering the remains of an old Klingon vessel on the outer skin of the asteroid/starship, the Enterprise sees that it is caught in a fine net of the superstrong metal, and also having its energy drained. To complicate matters, another Klingon vessel intercepts the Enterprise’s distress message, and decides that it can destroy the asteroid/starship and the Enterprise in one go. Inside the craft, Kirk and the away team find that the inhabitants do not realize they are in a spaceship, and the team gets arrested. The inhabitants are of a variety of types (but all winged humanoids), and they claim that they are reborn after they die. It turns out that the real sentient life force on the ship is a giant plant, known as the Father Machine, and the other inhabitants are creations it has made and have no real sentience themselves. After Spock mindmelds with the plant/creature it realizes the Enterprise crew are not a threat to it, and allows them to leave. It is not so kind to the new group of Klingons. [Dateline: Stardate 7502.9.]
At Starbase 13, Kirk meets Gilla Dupree (of the Jain religion) who is searching for her father, Jacob Kell, known unfairly as "Kell the tra