Spock (who is planning to enter the Vulcan Science Academy) accompanies his father, Sarek, on a diplomatic mission to Marath, to settle a dispute between rival factions and pave the way for Marath to become a member of the Federation. There Spock gets to know a young Marathan named Cha-Tuan Mar Lorval, but although all sides sign the agreement, the faction that Cha belongs to seems put out, and tries to ambush the Enterprise (captained by Robert April and with Christopher Pike as First Officer) as they leave the area to transport Sarek and Spock back to Vulcan. Sometime later, Amanda is attacked on Vulcan, then Sirok (Spock’s cousin) is badly injured in mistake for Spock, as the Marath dissidents bring their fight to Vulcan, but they won’t say what their dispute is about. Spock recognizes Cha in disguise on Vulcan and slips away from the security of his house to try to find out what is going on. He succeeds in that but is injured in an assassination attempt (Cha saves him but is injured himself). Spock discovers that one of the Marathans was to have told Sarek about a sacred site that all Marathans should be granted access to, but he failed to pass on the message because he wanted the war to continue (and the others felt restrained by religious taboos). A codicil is added to the agreement and all is settled. However, Spock has now been offered a position at Starfleet Academy (after Robert April recommended him, after he had undone some computer sabotage by the Marath dissidents).
McCoy's first meeting with Kirk is during an unofficial nighttime football game that ends with both of them in trouble, and McCoy being "volunteered" for the Disaster Relief Service Club. He is not too happy when this results in him missing a trip home, and really unhappy when he almost falls from a ladder during training, when an earthquake shakes San Francisco. But worse earthquakes are shaking the planet Playamar, and the Disaster Relief Service Club get shipped off there to help in the rescue effort. On the planet McCoy's group (which also includes Spock and Lisa Donald) manage to rescue a number of people, but they find themselves in danger as the aftershocks continue. Spock is puzzled by the earthquakes on what was a geologically stable planet. When they have to use a forcefield brace, they notice the same ion storm effect that accompanies the earthquakes and speculate that the earthquakes are being deliberately caused by someone in subterranean caves. They (along with a security team) are sent to investigate, and they discover a group of Danai (who had previously made claim to the planet) operating a forcefield generator to create the shocks. The security team is disabled by the Danai, and McCoy, Spock and Lisa are trapped, but they succeed in ambushing the Danai and rendering them unconscious. With the aftershocks stopped, the rescue operation is able to complete its task, and the cadets are on their way home. McCoy hopes to get a date with Lisa, but she informs him that she has a boyfriend, by the name of James Kirk.
Cadet Kirk is disappointed when Dr. Daystrom is delayed, and he ends up piloting Ensigns Spock and McCoy to the conference at Colony Cambria instead. Also disappointed are Joe Swingle and his crew of pirates at Atlantis Station who are working for the Klingons and hijacking the shuttle Zodiac Spitfire with the three young Starfleet members aboard, while thinking they were getting Dr. Daystrom. Kirk helps lead the escape, helping to destroy the pirate’s base in the process as well as taking Swingle captive, and the Enterprise with Captain Christopher Pike arrives in time to warn off a Klingon warship and take the shuttle aboard.
Worf and his brother, Simon, arrive at Starfleet Academy and Worf immediately gets into a fight with a Brikar named Zak Kebron. Instead of dismissing them from the Academy, Worf and Zak are put as roommates. Meanwhile, Simon has set up a study team, including the seemingly spaced-out Mark McHenry, the Vulcan Soleta, and Tania, who seems to have a crush on Worf. During the year, the dislike between Worf and Zak does not diminish, and Simon seems to be struggling academically but Worf thinks it is a show to make Worf feel better. The study team and Zak get assigned to a mission to the outdated monitoring outpost known as Prometheus, and while they are there, they are attacked by a Romulan ship. Their commanding officer (Clark) is killed, and things look hopeless for the cadets, but they attempt to reach their shuttlecraft. Along the way Zak and Worf have to cooperate, and Worf is instrumental in saving Zak’s life at one point. But the effort seems wasted, as the Romulan ship blows up the station, but the station then dissolves away, and the cadets find themselves in a holosuite being greeted by the supposedly dead Commander Clark. Simon storms out in disgust and, to his own relief, resigns from the Academy. Worf and Zak won’t admit it, but their relationship has improved.
Trouble has been brewing between the Federation and Klingon members of a joint colony on Dantar IV, and Worf’s Academy team are sent to lend assistance, and hopefully get the two groups working together. On arrival, they find that the Klingons have also sent a team, led by K’Ehleyr, and also including Khard and Kodash. The two groups are left at the colony while the Federation and Klingon starships go off to attend to other business. The distrust among the two groups of colonists is, unfortunately, mirrored in distrust between the two groups sent to assist the colony (fueled in large part by the natural animosity between Zak, a Brikar, and the Klingons). However, the groups do work together, and the colony is starting to get in order when a spaceship starts firing on the colony. Now the two groups really have to work together to defend themselves, but the distrust is enhanced when the ship is identified as a Klingon design, but the weaponry shows as Federation technology. Nevertheless, the two teams work to get the phaser cannon back working just in time to cause the ship to crash out in the desert, as it appeared to be about to wipe them out. With the colony devastated, it is agreed that the best plan is to evacuate the colony, but the Starfleet and Klingon teams remain behind, as there is not enough space on the transports for everyone.
Marooned on Dantar IV the group of Starfleet Academy cadets and the three Klingons are still having problems getting on together, and the expected rescue is taking longer than they had initially imagined. While investigating the desert, Soleta comes across the remains of the downed starship that had been attacking the colony and is surprised when she is attacked by a survivor of the crash, but she manages to subdue him with the Vulcan neck pinch. She discovers, to Zak’s chagrin, that the attacker is a Brikar. The Brikar refuses to talk, but Soleta uses the mindmeld to learn that his name is Baan, and he was trying to reach a secret Brikar base, part of a plan by the Brikar to attack the Federation. The Starfleet and Klingon teams find and start to investigate the secret base, mainly to find the communication center and call for help. While most of them are in the underground base, Baan breaks free and operates a defense system which floods the base. Before they all drown, Worf uses one of the stored Brikar weapons to break through to the drainage system. Baan is recaptured, and the teams are rescued. They discover that the Brikar rebellion had taken place while they were marooned on Dantar IV, but the rebellion had been quickly put down. K’Ehleyr, who is part human, decides to join the diplomatic team working to sort out relations between the Federation and the Brikar.
Jack Pettey is a very competitive cadet, and Geordi La Forge gets on the wrong side of him when his elimination team beats Pettey’s. Then the gym class, including Geordi and Pettey, get assigned to a wilderness and combat training session on the uninhabited planet Saffair, which involves the ‘Capture the Flag’ contest. After Geordi (who was used to being on starships) behaves calmly during a simulated emergency aboard the U.S.S. Glenn (which is transporting them to the planet) he gets assigned as captain of one of the four teams. Geordi (who had always been seen as a bit of a misfit in sports because of his VISOR) picks the other ‘misfits’ in the group for his team, but they get through the first round with some inventive strategy and find themselves playing against Pettey’s team for first place. Coming up with some new ideas, Geordi’s team is victorious, and Pettey is a sore loser, but softens a bit when Geordi offers the hand of friendship instead of gloating.
Geordi is part of a field trip to Research Station Atlantis, which has a base station built on a volcanic island in the Atlantic Ocean and an underwater station two kilometers below the surface. Arriving at the base station they first prepare reports based on data from the base station, where Geordi and the Stenarios clones (Amril and Amray) come to suspect that the volcano is close to erupting. Ven of Almadixarian (an Andorian cadet who had refused to share piloting duties on the shuttle flight to the station), T’Varien (a Vulcan cadet) and Yoshi Nakamura (a Japanese cadet) maintain that all the readings are within normal ranges and nothing is going to happen. On a trip to the summit of the volcano a minor eruption occurs and Geordi saves Yoshi from falling over the ledge. Then they visit the underwater station, referred to as Neptune’s Locker and, while there, a major earthquake occurs, damaging the station and cutting off communications. The cadets and their instructor, Leilani Kamehameha, have to find their way through the icy water in the leaking station, with Ven injured and barely conscious, and others suffering from hyperthermia. Geordi, leads them to their shuttle and recovers data chips with the research data along the way, but then he, assisted by Yoshi and T’Varien have to go outside the shuttle in skin-suits to manually free the shuttle from the station (which had slid down and was precariously perched on two rock towers). They finally make it back to the surface to find the volcano had erupted and the base station had been badly damaged.
Data and four Yann (a race of clones, insular) are left on board the Yosemite after the crew mysteriously vanishes after encountering an unidentified alien spaceship. Another group of youngsters on the other ship (Osparrans - skeletal looking aliens) are also all that remains after their crew also disappears, but both groups make out they are the crews and threaten one another. Data finally grasps what is going on and calls the Osparrans bluff. Turns out both ships have been disabled by the T'chakat (leathery bulgy headed creatures with thin stalks of a neck, 6 tentacle arms) who have a force field that traps starships near their planet - they have had unfortunate encounters with warlike aliens. Data attracts their attention by trying to phaser through their force field and talks them into releasing both crews.
Data is among a group of cadets selected to travel aboard the starship, Republic (with Captain Clark), to view a super-Jovian planet ignition (the collision of two gas-giant planets, resulting in the formation of a new star). Approaching the system where the collision is to occur, a distress signal is picked up, which comes from a space station that has collided with an asteroid. Radiation prevents sensors determining if any life forms are aboard, and also prevents use of the transporter. Data is among those selected to board the station via shuttlecraft. On board the station, the away team splits into two groups to investigate. Data's team get attacked by lizard-like creatures and also discover some other unconscious life forms (humanoid, with pale yellow skin and large oval eyes). These latter creatures (the Umiiga), it turns out, have been rendered unconscious by the radiation, which also causes them to revert to the vicious lizard creatures. Dr. Steinberg, who is leading Data's group, is seriously injured by the lizards, and with the radiation preventing the communicators from working, Data decides the best way out is to locate the control center and get the station moved out of the asteroid belt, to enable them to contact the ship and get beamed off before the new star forms and destroys them. He has to subdue another cadet (Glen Majors), who doesn't think the plan is feasible, but they escape just before the planets collide, forming the new star, and they save the inhabitants of the space station.
Jean-Luc has just failed his first attempt at the Starfleet Academy entrance exam, and he had promised his father (Maurice) that, if he failed, he would stay on the vineyard. However, Jean-Luc knows that the only future that would satisfy him is one in space and he secretly applies for the following year's exam (this time to be taken at the European examination site in Paris). His friend Louis gives him the ideal opportunity to put in his application, and Maurice wins a prize for his wine, and is invited to address the winegrowers in California, just at the right time for Jean-Luc to take the exam without his father knowing. The tests are going reasonably well, and Jean-Luc is fairly happy with the outcome of the command test, when he arrives back at his quarters to find his father waiting for him. Someone from Starfleet had wished his father well on his son's latest attempt at entry into the Academy, and he had immediately returned to France to take his son home. Jean-Luc, however, insists on completing the exam, even though his father says he will not be welcome home again, even if he fails. The psych test was supposed to be the next day, but although the other cadets were sent off to their various assignments, Jean-Luc was sent to Counselor Trevalion who asked him what his plans were after failing the Academy exam a second time. Shaken, he told Trevalion that he would do whatever was necessary to get into Starfleet; he would be back the next year to take the test again. That turned out to be his psych test - facing his fear of failure. His father did allow him home again while he waited for the results to come through, and when they did it was a call to be at Starfleet Academy in three weeks’ time to begin classes.
Jean-Luc Picard is struggling through his first year at the Academy, but always ends up in second place behind Roger Wells in class. Nevertheless, he finds himself selected to fly with the Nova Command team, along with his friend, Marta, but then finds he is on a ship with Roger as second-in-command. Roger becomes acting captain when the Kemoran captain, Tabath, falls ill and goes dormant. They then receive a mayday call from two miners in the asteroid belt who have a disabled craft and a black comet bearing down on them. Roger is unwilling to take action, but Jean-Luc privately suggests a course of action that enables them to save the miners and complete their mission, even if they do arrive four hours late with their ship, the Ishtar, in a rather sorry state after a rough ride towed by tractor beam attached to the black comet. Jean-Luc and Roger become friends, even if they do continue to compete with each other to some extent.
Beverley and her roommate, Claire Voy, both get into trouble for skipping a class, and are then both involved in mishaps in holodeck simulations. Beverley receives an electric shock, and another cadet, Peter Peterson, is injured, and the teacher, Commander Max Wiley, blames Claire (who was in the simulation with Peter). Wiley is himself held responsible, since he was in charge of the simulation. Beverley and Claire set out to do their own investigation of the incident but get in more trouble when they are discovered making an unauthorized copy of the simulation program. But with the help of Data and Mrs. Oner (actually an ambassador for her planet, Muldan, but who runs a restaurant), they discover that the incidents were caused by a computer virus introduced by another cadet, Stephen Cody, who was trying to discredit Commander Wiley.
Young Will Riker joins the Academy jazz band, which also has Geordi La Forge as a roadie. Riker is dismayed at the practical jokes played on him as the “new-boy” but gets his own back before the bands opening number in a contest on Pacifica. An Orion judge, Jaktu, asks if the band can play at an Orion outpost, but is told that he will have to go through official channels with his request and that the band couldn’t go straight on to the outpost after the contest anyway. So, Jaktu attacks the band’s ship, the Gallant, as they are leaving Pacifica and tows them to the outpost, a planet called Elofim in the Zyrapul solar system. There they find a war-weary troupe of young Orion mercenaries who really appreciate the band’s concert, but right at the end of the concert they all come under attack from enemy aircraft. Geordi and Will shelter in a partially destroyed building, and discover a robot rat-like surveillance device, which Geordi manages to disable (if only temporarily) with an electronic instrument (a Coridan phase modulator) that he has. He later uses the same instrument to cause one of the enemy aircraft to crash. They discover that the aircraft is also a robot-controlled craft, which uses Federation technology, so they decide that they would not be breaking the Prime Directive by interfering. Consequently, Geordi uses his Coridan phase modulator to cause the robot army to surrender. It turns out that the robots were owned by a group of Tellarites.
Deanna Troy had enrolled in Starfleet Academy partly to get away from her overbearing mother, but then finds that her mental shields are not developed sufficiently to protect her from the human emotions surrounding her, and it is affecting her work. A counsellor, Lieutenant Commander Thaddeus Gold, assigns her to a study group that includes her friendly Ichthyan roommate (Twil d-ch-Ka, who gets known as Auburn), a guy who accuses her of being a mind reader (Alex Renny), a Xybaki male who keeps making unwanted amorous remarks to her (Vandin ua Xadmy Sidk), and a Zakdorn male (Tronnald First-House). To make matters worse, her mother (Luxwana Troi) gets a job as a lecturer at the Academy to keep an eye on her. Deanna decides the best thing she can do to prove her independence is to apply to take the Borocco-Kai test (commonly known as the Big Washout) in this first year, rather than in the normal second. She talks her study group into taking it with her, and when it comes time to take it, Auburn is assigned the role of leader (much to the chagrin of Vandin, who considered himself a natural leader) and their task is to rescue an Alpha Centurian freighter, the Borocco-Kai, that has been taken over by Orion pirates (it’s all a holodeck simulation of course). They all become prisoners of the Orions but, with Deanna’s insight, they locate a hidden ventilation duct that first leads them to the one remaining freighter crewman (Bodrik Denbugh, ship’s engineer, who can tell them about the ship’s layout) and lets them escape. Most of the team manage to escape from the freighter, although Auburn sacrifices herself for the others, and Vandin gets himself ‘killed’ by the Orions unnecessarily, and he ends up as the only one of the group to fail the test and has to leave the Academy. After seeing what her daughter had achieved, Luxwana finally, and somewhat reluctantly, acknowledges her daughter’s wishes.
Geordi is among a group of cadets manning the oldest ship in Starfleet, the Benjamin Franklin (Daedalus-class, launched in the year 2179, 175 years ago), on a training mission to map a section of the asteroid belt. Geordi starts out as a hero, when he leads the rescue of an Andorian cadet, Trennek, whose airline comes loose from her spacesuit. He also gives a presentation about the history of their ship and its first captain, Ikushima. However, his future in Starfleet comes into doubt when he believes he sees Captain Ikushima, who is long dead. The situation changes when Hassan, a cadet who is acting as Chief Engineer later sees the same image, and then the whole crew sees it (although Sanchez, the acting Captain, sees his father, not Ikushima). They determine that they are being affected by some sort of beacon emanating from the asteroid Siva. On the asteroid they discover a small escape-pod type craft that has apparently been there for six hundred thousand years. Due to the discovery, they are given a hero’s welcome when they arrive back at Spacedock.
It is three years after Data was discovered on Omicron Theta, and he starts keeping a journal. He becomes part of an Academy class research team sent to the planet Arunu to investigate ancient ruins where they meet up with an archaeological team, who have discovered that the vanished Arunians used to communicate through emotions. They have discovered some artifacts, called tsidi, which appear to be some form of “emotion battery”, and Data turns out to be one of the few people (along with the unemotional Dryondites) who can handle the objects without being affected, but the Dryondites seem to be unwilling to let Data participate in their work. Data modifies an instrument called a tee qitm so that it can register emotional energy over a large distance, and discovers a cave giving off strong emanations. He and the cadets investigate and discover three Dyrondites doing something with the tsidi “batteries”, and the Dryondites capture Data and the cadets, imprisoning them in the caves. In trying to find a way out, they discover a cave filled with tsidi that had been broken. Data comes to the conclusion that the tsidi were a form of dump for the Arunian’s negative energy, and that the Dyrondites were planning on using them as a form of weapon. Data escapes and warns Professor Spinaker of what is happening, but there seems to be no way to stop the Dyrondite warship that is coming to collect the tsidi. Data manages to convince the Dyrondites that he has switched allegiance to them, and smuggles a small unit aboard their ship, but he has been beamed to a ship in orbit, not the smaller vessel collecting the tsidi, but he uses the cobiem charge to cause a disruption on the vessel, leading to the vessel being evacuated. Spinaker manages to round up the other Dyrondites.
O’Brien’s young daughter, Molly, supposedly has an invisible friend (who she calls Dhraako), but then Nog sees this ‘friend’ and thinks it is a Ferengest (a Ferengi vengeful ghost) and he runs away screaming, with ‘Dhraako’ following him. Jake tracks the scared Nog down and finds that he can just make out the ghostly image in dim light. The ghostly person beckons for the two to follow him, and Jake agrees while Nog goes to try to get help, but nobody seems to want to take him seriously. The ‘ghost’ takes Jake to a disused area of DSN that it uses as a base and, using a transparent control panel, moves Jake into his own plane of existence in order to converse with Jake. It explains that it is a Quester, part of the Dhraakellian Whole, and had come to the station (through the wormhole) during its Cardassian days as an observer and had been there since. It could be seen by very young kids, but not by adults, since it was on a different plane from the normal physical universe. It was trying to pass on a warning that a group of Cardassians who were visiting the station (led by Gul Chok) had planted explosive devices near one of the damaged reactors. He shows Jake where the bombs are, but now Jake cannot be seen by adults. He manages to get Nog to overcome his fears of the ‘ghost’ (and to Jake’s own ghostly appearance) and have him tell his father (Sisko) and O’Brien how to retrieve Jake using the transporter. They then locate the bombs with minutes to spare and beam them off the station, where they disable Chok’s ship, and the Cardassians are taken into custody. As an observer, Dhraako is not supposed to be known to the locals, so he leaves to observe elsewhere.
Dr. Bashir takes a trip to Sakelo City on Bajor, a town known as a "hotbed of revolt", and Jake and Nog stowaway on his shuttle. Bashir gets kidnapped by Tikar Antol, a rebel leader opposed to Bajor's association with the Federation and equally opposed to Bajor's religious establishment. His group is called the Turnaways, and they are based somewhere outside of Sakelo City but their camp is hidden by a stolen cloaking device. Jake and Nog meet a local girl, Sesana, who leads them to the camp and finds out where Julian Bashir is being held. While she goes back to town to get help, Jake manages to free Bashir after Nog creates a diversion by starting an avalanche down the sides of the valley in which the camp is based. Nog gets captured, but Bashir and Jake commandeer one of the rebel's vehicles and a couple of phasers and together they free Nog and destroy the cloaking device. In disrupting the rebel's camp, they also thwart an assassination attempt on Carik Madal, who was about to be installed as a Vedek, and an attempt to kill everyone on DSN with a vandellium bomb (which vaporizes living tissue but doesn't affect other matter). Nog talks Bashir into keeping quiet about the boys’ actions, so that Sisko (who has been away on a mission) doesn't hear what his son has been up to.
Centered on Jake and Nog and an obnoxious young Bajoran boy, Riv Jakar, and a young Cardassian girl, Kam Gavron, who had run away from her father who is Gul of the Third Fleet. Riv kidnaps Kam, but Kam is rescued, largely by Jake, just before Gul Gavron blasts the station. A repentant Riv (whose life had been saved by Kam) provides a safe cover story for Kam to tell her father.
Jake and Nog rescue a sort of mini-rhino that is being ill-treated by its master, who had stolen it from a planet in the Gamma Quadrant. Later, the animal, called Babe, escapes when the man tries to recapture it. A craft, like a giant sphere, comes through the wormhole. The occupants, with heads like throbbing energy bubbles, demand the return of their prince, and start to destroy DSN when nobody is able to comply. Jake and Odo find the missing Babe, who is undergoing a transformation wrapped in a cocoon of golden hair, emerging as the slender Pyxian prince Joryl. The attack turns out to have been illusory.
Jake, Nog, Tina Lin (a Bajoran girl) and Rotor (a reptilian Selay boy) are frequent customers at the Games Bazaar, run by Bokat (a Ferengi). Bokat offers Jake a free trial run on a new game he has, The Zhodran Crystal Quest, but Jake has promised Sisko he won't play any more games at the Bazaar until he has finished a history assignment. In the meantime, the other three children are found with various injuries and in an unexplained coma. Jake discovers that their minds are trapped in the Zhondran game, which is actually a test for other civilizations set by the wary and insular Zhodrans. Jake convinces Sisko that the only way to free the other children is for him (Jake) to play and win the game, which he does, and wins the right to open negotiations with the Zhodrans.
Keiko O’Brien arranges a field trip for ten of her students to Cetus Beta in the Gamma Quadrant. That planet was chosen because it only has plant lifeforms, although some of them can move about, but none are life threatening. The most dangerous plant is a Tingle Tangler, which can deliver an electric shock. However, as the runabout approaches the planet, a Cardassian ship emerges from the planet, and shoots them down. They all survive, although the pilot is badly injured, and they then find all their electronic equipment is being stolen by someone. Nog sets a trap, and they discover that the thief is a Trofar named Lek. The Trofars are short (about one meter tall), hairy, humanoids, that have been biologically adapted by the Cardassians to require electronic implants. These implants enable them to avoid detection by sensors, and the Cardassians had planned to use them as spies, but the Trofars had managed to escape from them. Now the female Trofars are about to give birth, and the electronic equipment had been taken to make implants for the babies, who would otherwise die. The children, along with Lek, capture the Cardassian ship, and they make their escape.
Jake and Nog get kidnapped to the homeworld (in the Delta quadrant) of the Fjori (a gypsy-like race) after Nog tries to discover the location of the homeworld (named Ryft, meaning Eden). They are sentenced to spend the rest of their life there, until someone suggests that they take the Rite of Passage which would qualify them as Fjori and enable them to