The Enterprise manages to bring an out-of-control starship, the Sphinx, back under control, but finds the crew dead and the captain had been killed by someone (unidentified) who was lying dead near him on the bridge (the life support was not working). Scotty discovers indications that the ship had been in proximity of a cloaking device (the Enterprise had captured a cloaking device from the Romulans not long before this). The investigation of what had happened to the Sphinx is handed over to Gahe Darres at Deep Space Station M-20, but Darres dies from an apparent transporter accident after telling Kirk he needed to see him urgently about something he had discovered (which Kirk realizes later is to do with an autonomous investigative agency mentioned in Section 31 of the Starfleet charter). Spock visits the Romulan Commander that the cloaking device was taken from, and who had not yet been transferred back to the Romulan Empire, to see if she can provide any information on how the Sphinx might have come into contact with a cloaking device. There was a scientific conference going on at M-20, and Kirk meets up with a lady scientist, Dr. Jain Suni, who is working with Bendes Ketteract, and Ketteract makes a statement at the conference that is very derogatory of Starfleet’s ability to face the threats posed by the Romulans and Klingons. Ketteract and Suni then get called away by an urgent message. Meanwhile, Dr. McCoy is trying to locate another doctor, Dr. Karen Nico Patterson, who he believes might be able to help him with the fatal disease, xenopolycythemia, that McCoy has just discovered he has. McCoy enlists the help of Chekov in locating her and Chekov traces her route up to the point where she, and several other scientists, had been picked up by the Sphinx. Since Ketteract had been involved in studying the cloaking device for Starfleet, Kirk believes that he was probably involved with these recent events, and thinks it likely that it has something to do with a highly unstable omega molecule that he had postulated about in the past. The Enterprise sets out to try to track where he and Suni went, using the path that the Sphinx had emerged from as a guide. They reach the region where they believe Ketteract’s base might be, but nothing is visible although Spock identifies a cloaking field. After locating where the center of the field is, they are able to transport the cloaking device out and expose Ketteract’s space station. The experiments with the Omega molecule are coming to a conclusion and Kirk and a team board the station to try to terminate the experiment. Suni sets the implementation off and the Enterprise team are able to beam off the station and get the ship away before the unstable element destroys the station and creates an expanding field that threatens the subspace continuum. The Enterprise crew are able to use the cloaking device in conjunction with a subspace transceiver and an energy converter to stop the spread of the field, but a zone of space is left where warp travel is impossible. [Timeline: Stardate 5462.1]
The Enterprise is on its way to the Paragon Colony on the inhospitable planet Sycorax, a colony that is considering joining the Federation but which has been involved in human genetic engineering. At Spock’s suggestion, Kirk starts to review the history of Earth’s experiments with eugenics, recalling how Gary Seven, Isis and Roberta Lincoln had discovered the plot by Dr. Sarina Kaur to breed a group of genetically enhanced children (two hundred and sixty four had been born by that time), and planned to spread a disease, using genetically modified streptococcus, to kill off a large portion of the normal human population to make way for her special group. Seven had been able to cause the facility’s nuclear power plant to explode, destroying the facility (Chrysalis Base) in India, and had the children transported out and set up with foster families through an orphanage. Many of the children were suffering from psychological disorders, but one, known as Noon, was particularly bright and Seven hoped to train him as an agent. As he grew, Seven took Noon on a few missions but became discouraged at Noon’s ruthlessness. On one of the missions they met up with an eternal scientist, known at that time as Dr. Wilson Evergreen and whose inability to die was discovered when Noon tried to kill him. Evergreen had planned to use his knowledge to control the hole in the ozone layer, but was talked out of it by Seven who showed how people planned to use the technology as a weapon. Noon, who later insisted on using his first name of Khan, then started to develop his own organization and invaded Seven’s office while Seven was in Europe during the breakup of the Soviet Union. There he discovered the location of Dr. Evergreen and of the other genetically enhanced children, before shooting up Seven’s computer, Beta 5. During the time Kirk has been reviewing these events, the Enterprise has arrived at Sycorax and discovered that the Klingons (led by Captain Koloth and his second in command, Korax) were also there. The Klingons are told to leave Sorcorax after Korax is found committing espionage, but soon after that an explosion damages a power plant connected to the shield that protects the inhabitants of the Paragon Colony from the Venus-like atmosphere. [Timeline: Stardate 7004.1 when Kirk is en route to the Paragon Colony, four years after the encounter with the Botany Bay; year 1974 when the Chrysalis Base complex was discovered, to 1989 when Khan destroys the Beta 5]
The Enterprise crew manages to help the inhabitants of the Paragon Colony come up with ways to protect and repair the colony’s shield, and the Enterprise drives off the Klingon warship. Then Kirk goes back to considering the application for Federation membership from the Paragon Colony, while reviewing the events of the Eugenics Wars. With the information that he stole from Seven’s computer, Khan brings together a number of the children of Chrysalis, but others have been building their own power bases and want nothing to do with Khan. Khan has launched a satellite (Morning Star) with the ability to destroy the ozone layer, either selectively or completely and he considers using it on the Balkans after one his Chrysalis siblings, Hunyadi, tried to kill him by creating an earthquake while he is having a meeting at Ajorra. Khan escapes and is talked out of using his Morning Star satellite by his Egyptian associate, Ament, instead attacking Hunyadi’s base by submarine. However, the submarine gets sunk, with only Khan escaping from it. Another of the children of Chrysalis, Morrison, has established a paramilitary base in the US and begins using sarin against what he considers symbols of the world-dominating authority, but he commits suicide after Seven and Roberta (and a little help from Guinan) thwart his plans. Dr. Donald Archibald Williams brings Khan the secret of the necrotizing fasciitis virus, but ends up having it used on him after Khan’s medical expert has perfected it. Khan develops a base on the old French nuclear testing base at Muroroa Atoll, and plans to use the necrotizing fasciitis to wipe out the general population (who are starting to move against him). A group of Chrysalis women, known as Amazons, attack Khan’s Muroroa base (after a tip-off from Roberta) and destroy the base minutes before the rockets were to be launch to wipe out the general population. In frustration, Khan initiates the destruction of all life on Earth, using his Morning Star satellite, but calls it off after Seven offers him the use of the DY-100 sleeper ship to escape and set up his own colony on an uninhabited planet. The DY-100 had been developed secretly by the US at Area 51, using information gleaned from the encounter with the Ferengi at Roswell and with tips passed on through Roberta (Seven saw the ship as a possible way to save some of humanity if an all-out nuclear war occurred). It turns out that Isis (Seven’s cat) had infiltrated Khan’s organization as Ament, but she gets killed by Khan’s bodyguard while trying to protect Roberta. Seven, who is getting old, retires back to wherever he came from, and Roberta is promoted to become Supervisor 368 and is soon joined by Rain Robinson, who was a member of SETI and had noticed mysterious goings on, including the departure of the DY-100. Kirk decides against Federation membership for the Paragon Colony after a visit from Seven, who points out the arrogance that the genetically enhanced have.
While the Enterprise-A is being prepared for service, Kirk feels a need to visit Ceti Alpha V to try to find out what happened to Khan Noonien Singh and his colony, and Spock, McCoy and Sulu accompany him. While Sulu waits in orbit in the cruiser (Yakima), Kirk, Spock and McCoy beam down and find the recycled cargo carriers used as shelters and inside find a trap door leading into caves below ground. Down there, they discover a hidden mausoleum containing Marla’s coffin and Khan’s diary, along with data disks that Marla had recorded. From this data they discover how the colony, New Chandigarh, started out with hope, but some dissent (led by Harulf Ericsson), and a general distrust by most for Marla. The latter led to Khan banishing her from the colony after she stood up for Zuleika, who Khan had accused (unfairly) of trying to murder Marla, but after Khan realizes he had erred, he rescues both Marla and Zuleika. They have to ration food initially, but get a good crop growing. Then they have a mass wedding, but the end of the celebration is disrupted when a native ‘bison’ stumbles through the group, and it is later found that it has a parasitic ‘ceti eel’ in its brain. Soon after that, Ceti Alpha VI is seen to explode, and then earthquakes and volcanic activity start to wreck their planet (Spock later speculates that a small black hole had passed through the system) and Khan’s colonists have to vacate to the caves to survive. Six months after they were abandoned on the planet, the ‘nuclear winter’ environment that follows the earthquakes, etc., kills off most of the native wild life (except the ceti eels unfortunately) and the colonists are left trying to scratch an existence from the dying planet. They establish a colony, called Fatalis, in the underground caves. Ericsson later tries to stage a revolt against Khan by infecting Marla with a ceti eel and ordering her to kill Khan, but her mind is able to regain control of her body and she kills herself rather than Khan. Ericsson and his followers escape, and Khan is unable to track them down until they take over the Azar Gorge (five years after Marla dies), which is the colonists’ main source of water. Inspired by the story of Kirk’s triumph over the Gorn, Khan improvises explosives and is able to retake the gorge, killing Ericsson and most of his followers, but the younger members of the rebels are led to safety. This band of youngsters (led by Astrid, Ericsson’s daughter) seize Kirk, Spock and McCoy as they are studying the find at Marla’s tomb, and they demand to know where Khan is. They initially refuse to believe that he can be dead, but Kirk tricks the youngsters into taking them to the planet’s surface, supposedly to signal Khan to come down, but actually to get Sulu to rescue them. The Federation resettles the survivors of Khan’s colony on Sycorax, which already had a colony of genetically engineered superhumans. [Timeline: Stardate 8415.9 when Kirk visits Ceti Alpha V, a year after Khan dies; Khan’s colony on Alpha Ceti V established in 2267; Marla died in year 2273]