Jurai follows Azusa, the Emperor of Jurai, and details his life up until he becomes emperor over 700 years ago—from his upbringing as a boy brought to Jurai by Lady Seto, to his exploits as a twenty-one year old crown prince who battles the powerful pirate Kagato and later falls in love with a simple Earth girl named Funaho.
Azusa, the Emperor of Jurai, has been visiting the Masaki household on planet Earth every day for the past week. Each day follows the same routine: Azusa forbids his daughter Ayeka's relationship with Tenchi Masaki unless the boy can defeat the suitor he brought for Ayeka in a duel. However, every attempt to have this duel has been interrupted by some outrageous event.
Today marks the eighth duel in a row and proves to be no different from the previous ones. Despite Azusa arranging the time to be different every day, Mihoshi again suddenly crashes her spaceship into the pond and sends Tenchi and the suitor into the water; as Tenchi gets out while the suitor remains unconscious, he is once again the winner.
Unfortunately for Azusa, after eight consecutive failures, he's exhausted his monthly income and can't get any more suitors for the time being.
Thankfully, he can still enjoy the celebration that his second daughter Sasami has invited him to for the eighth day in a row, along with his two wives, Funaho and Misaki. At the party, a drunken Ryoko accidentally throws a two-liter bottle of sake at Azusa's head when she tries hitting Ayeka. Meanwhile, Mihoshi and Misaki drunkenly introduce themselves to each other the entire night, not meshing their sentences together yet somehow perfectly understanding each other. The alcohol-fueled pandemonium is only temporarily interrupted when Ryo-Ohki, in her child form, performs "I'm a little teapot" for Azusa, who puts up with it knowing that Sasami would be mad if he made her cry.
Come next morning, it's time for Azusa, Funaho, and Misaki to leave, though any potential emotion in this departure is absent considering they've done this eight times now. While Azusa and Funaho try to depart silently, they have to drag Misaki with them because she is still incoherently chatting with Mihoshi.
After they leave, Tenchi begins thinking about his family, including his grandfather Katsuhito—who he thought was just an ordinary guy until he learned he came to Earth 700 years ago. He also thinks about his ability to generate Light Hawk Wings, though he's only done it twice since it has no purpose in his ordinary life. Furthermore, he's amazed that, to him, it feels like the many people living with him have always been here, despite it having been only a year, and he wonders why it's so much fun. Sasami snaps him back into reality, and he goes to work in the carrot fields for the day.
Traveling aboard his Royal Tree Ship Kirito, Azusa, the 21-year-old Crown Prince of Jurai, suspects that the "old bat"—otherwise known as Lady Seto Kamiki—is tracking his ship's location and is passing it on to an abundance of families. These families proceed to stage mock pirate attacks to get Azusa to "rescue" them, only to try and wed their daughters to him to so they can obtain fifth or later generation Royal Trees. While Seto, in a mischievous fashion, might be trying to help him associate with a woman other than her three-year-old daughter Misaki—his fiancée, Azusa knows better. Seto's "Operation Arranged Marriage" is just a prank designed to keep tabs on him while he wanders in space and away from Jurai's politics.
Jijii, Azusa's guardian unit, now informs him of a real pirate alert. When they arrive on the scene, however, they find only the wreckage of the escort fleet that sent the signal, as well as the massive white battleship that attacked them, but it looks and behaves nothing like a typical pirate ship. Jijii advises Azusa to attack immediately, but Azusa is curious and instead wants to meet the people onboard. They teleport onto the ship, and after Azusa destroys more than 200 robot guards barehanded, they enter a subspace hole that brings him to a hall where a man is playing the pipe organ.
The man introduces himself as Kagato and claims he only seeks to "liberate" knowledge for those who deserve it and store it in his ship, the Sōja, and he does not consider his actions to be piracy. Azusa disagrees and challenges Kagato to a fight, but he vastly underestimates Kagato's power, and he can't harm because of his incredible regenerative ability. Just as Azusa is wounded when he and Kagato simultaneously strike swords, Kirito intervenes when it suddenly appears inside the Sōja opens and opens a path for Azusa and Jijii to enter.
Azusa and Jijii return to Kirito's bridge and heavily damage the Sōja in battle, but they're suddenly attacked by the spaceship Ryo-Ohki, commanded by Ryoko. Ryo-Ohki's powerful attacks prove overwhelming even for Kirito's Light Hawk Wings, but their fierce exchange of energies creates a tear in the fabric of space and engulfs all three ships. While both Kagato and Azusa see a glimpse of Tsunami, the progenitor of the Royal Trees, Azusa saw Tsunami morph into Mitsuki, a woman dear to him that he hadn't seen in a long time.
Jijii wakes up Azusa from his sleep, and the narrator tells what had and will happen. Kirito, Ryo-Ohki, and the Sōja all disappeared from where they were battling. Tsunami would assimilate with Azusa's future daughter Sasami in 50 years. For the moment, Kagato needed to repair Sōja, but he became interested in the Royal Trees, later ordering his servant Ryoko to steal Tsunami—the mightiest of all trees on Jurai. And lastly, Ryo-Ohki's lifespan was shortened after the battle, causing her to eventually regenerate into her second generation after a spat between Ayeka and Ryoko.
Azusa and Jijii find themselves near a distant Juraian Colony world—one later known as Earth. They learn this planet was seeded with humans by the Great Prehistoric Civilization, but they find its registration strange. The planet's application is hundreds of years old but was only accepted last year, almost as if someone had wanted to hide it.
Jijii detects an energy anomaly on Earth's surface and Azusa, believing it to be poachers attacking the research vessel that registered the planet, goes down to deal with them despite being seriously injured after his battle against Kagato. Descending onto Earth, he runs into a group of pirates chasing after a girl. He dispatches most of them, but one of them shoots him with a stun gun, which, exacerbated by his wounds, makes him fall unconscious soon after he escapes with the girl.
Azusa wakes up in a room of a quaint house nestled deep in the mountains. Asumi, the girl's grandfather, greets him, but he tells him that he must leave as soon as he is well enough. Azusa also learns that the girl's name is Funaho, but he wonders why he mistook her for his lost love Mitsuki when Funaho held his hand while he was dreaming.
Over the next few days, Funaho gradually warms up to Azusa and begins voluntarily visiting him while he recovers. It becomes clear to Asumi that Funaho has certain feelings for Azusa. Thus, he tries to keep her from asking him too many questions about his family, including the woman named Mitsuki, whom he was mumbling about in his sleep.
Nonetheless, Azusa finds the opportunity to talk to Funaho, and he first asks her about her family. She tells him that her mother died shortly after giving birth to her sister and that her father never returned from attempting to slay "Orochi"—the mythical eight-forked serpent. However, Azusa is aware Orochi is actually a space pirate weapon and that non-bioroid primitives like Funaho's father would've been captured instead of killed due to their value. Thus, he tells Funaho he believes her father is still alive.
He then tells Funaho about his family with embellished names and titles. He explains how his father, Kazuki Yotsuga—then a Galaxy Police cadet—and mother, Amame Masaki, met and soon married, mentioning how Amame had to leave the Imperial Family to marry a commoner. Eight years later, after Azusa was born, Lady Seto Kamiki approached them and suggested that he become the next head of House Masaki. However, doing so would require him to rejoin the Imperial Family (as he inherited his status from Amame) and be separated from his mother—who hadn't received permission herself.
Naturally, the young Azusa refused to go along, but that changed two years later when pirates attacked the colony world where Azusa and his parents lived. Though trained to fight, the boy was nearly overwhelmed by pirates until Seto suddenly appeared and dispatched all of them herself. Azusa then confided to her that he wanted to be strong enough to protect his mother and the others, and he willingly accepted her invitation to Jurai.
Just as Azusa finishes telling Funaho his story and tries giving her a comb as a farewell gift, a single feathered arrow with a note attached strikes nearby. Asumi demands that Azusa leave immediately, but when pressed, he tells him the whole story of what's happening: the serpent Orochi appeared in the mountains about a year ago, and the bandits, serving as messengers, began making demands for treasure and young women. The warriors sent to defeat Orochi never returned, and the villagers who feared it left one by one until only Asumi and Funaho—who refused to abandon her grandfather— remained. Now, Orochi wants Funaho as a sacrifice.
Feeling he has mostly recovered from his wounds, Azusa tells them that he will defeat Orochi, but they beg him not to fight, and they resort to drugging his food when they later eat to stop him. As a Juraian warrior, Azusa is only mildly affected by the drug, and he fakes being asleep as Asumi tells Funaho that he will defeat Orochi. He tells her to run away with Azusa, and he subdues her when she tries stopping him. When he leaves, Azusa gets up and decides that he will ignore his wishes and fight. He runs outside and contacts Jijii, explaining the situation to him and getting Kirito to detect the pirates.
At midnight, Asumi arrives where he was supposed to bring Funaho and begins battling the eight-headed serpent, but his sword shatters when he strikes its metallic body. Orochi's laser nearly kills Asumi before Azusa protects him with his Light Hawk Wings, and the young prince outmaneuvers the machine in the dense woods and disables it. The pirates' attempt to take Funaho hostage goes awry when Kirito captures the ship controlling their operations from space, allowing Azusa to dispatch the rest on the ground and save Funaho. Joyous that her father is safe, Funaho embraces Azusa, all but confessing her love for him out loud.
Azusa spends the next few days at Asumi's residence waiting for everyone he'd rescued from the pirates to recover from being put in stasis. He realizes that he loves Funaho, but he can't bring himself to take her to Jurai, as doing so would separate her from her family. However, while hiking in the mountains, a pirate tells Azusa that he and his comrades have captured Funaho. He surrenders and gets escorted onto a ship, where he learns his captors are from the Shank Pirate Guild and are going to use him to negotiate with Jurai. They put him in a time-stopping capsule after confiscating his master key, but even without it, he can maintain his connection to Kirito. The ship locates Funaho via the comb Azusa gave her— one carved from a Royal Tree. He realizes the ship Funaho is on is too close, and she might get caught in his attack, but he suddenly hears a mysterious voice in his head offering to help him. Azusa proceeds deliberately attack and destroys the ship holding him, and with with Kirito's help, he transports directly to where Funaho is and envelops the two of them in the Light Hawk Wings, protecting them as Kirito destroys the Shank pirate fleet.
Together with Funaho, Azusa tells him everything she'd wanted to know about him without embellishment. Funaho then asks him about the woman named Mitsuki, whether she is his sister or his wife, and if she's worried about him.
With a saddened voice, Azusa tells Funaho that Mitsuki died eight years ago, and he offers to tell her a story while Jijii is still looking for them.
After accepting Lady Seto's offer to become the head of House Masaki, the young Azusa receives an impressive welcome on planet Jurai, but soon goes red with embarrassment when he realizes that the ribbon Seto put on his head is meant to look cute!
Shuzen Amaki, one of the Imperial Family members who opposed Azusa returning as heir to house Masaki, tries telling the Emperor of Jurai to stop all of this. However, even the Emperor can't help but laugh when Azusa calls Seto an "old bat" to her face because of the ribbon, and he goes off to arrange the boy's welcoming party.
Azusa finds his new life on Jurai filled with intense training. Seto, his teacher, accompanies him at all times, though he often tries running away from her and her antics. One day three years into his training, Azusa is doing precisely that, but he gets caught and teleported by one of his transport pad traps that Seto used against him. However, instead of seeing Seto, he finds himself in a garden and becomes fixated on a woman playing the lute nearby, who soon invites him to come and talk to her.
Her name is Mitsuki Amaki, and Azusa finds her beautiful despite her frail health. After talking with her for some time, Azusa has to leave, but Mitsuki mysteriously asks that he keep meeting her a secret. He promises to visit again, as meeting her made him realize, for the first time, he was glad he came to Jurai.
One night, Mitsuki takes Azusa out to a terrace to enjoy the view, but while she's in the middle of telling him a folktale about the moon's fog seal, she suddenly gets dizzy and falls to her knees. However, she insists that she's fine and tells Azusa to run away when she realizes someone is watching them.
Worried, Azusa skips the next morning's training to see Mitsuki again, but along with her, he unexpectedly meets Shuzen. He tells Azusa that he committed a serious crime simply by entering this garden. As he explains, Mitsuki has a unique ability: she's able to merge her consciousness with Tenju—the massive tree housing the Imperial Palace—and access untold amounts of classified information. At one point, when Mitsuki was very little, a member of House Masaki tried using her in a plot to overthrow the then–Emperor. Mitsuki was confined to this garden after that incident, with only the current Emperor being allowed to see her.
Shuzen berates Mitsuki and accuses her of drawing Azusa to her garden out of loneliness (which Mitsuki admits is the truth), even calling her a "shameless whore". Azusa becomes enraged and challenges Shuzen to a duel, but Shuzen is slightly more skilled and wounds Azusa. Only Mitsuki's intimidating aura keeps Shuzen from killing Azusa, and he happily leaves.
Azusa wakes up inside the palace prison, as Shuzen reported the incident, but he puts Seto's training to use and "talks" to the tree the prison is carved out of and convinces it to let him go free. He finds his way back to Mitsuki's garden and finds her speaking with the Emperor—her grandfather— telling him she wishes he'd let her die and avoid this suffering. Azusa confronts Mitsuki after the Emperor leaves and brazenly invites her to escape Jurai with him, saying that he doesn't care about the Imperial Family or becoming Emperor. Seto suddenly sneaks up on them and tells Azusa that he can't take Mitsuki with him. Undeterred by her powerful presence, Azusa tries fighting her with his sword, but she quickly subdues him.
Azusa again wakes up grounded in his room but is set free after a few days so he may attend a supreme council convened by Jurai's parliament that will determine his punishment. There, Azusa is surprised to find Mitsuki, but even more surprised to learn that she is the head of House Amaki. The Emperor arrives at the council, but he shocks everyone when he casually announces that the case against House Masaki (and, by extension, Azusa) has been dismissed. Shuzan angrily demands an explanation, and Seto privately talks with him inside a time-stopping force field, saying that she and the Emperor know that he and a spy of his had entered the forbidden garden along with Azusa. Thus, under threat of blackmail, Shuzen rescinds his complaints.
As it turns out, the actual topic of the supreme council was to arrange a tree selection ceremony for Azusa. Later, Azusa returns to the garden but only finds Seto, who tells him that he'll see Mitsuki tomorrow at his ceremony.
The next day, Azusa is glad to see Mitsuki amid the crowd that gathered for his ceremony, but he can't speak with her at the moment. He then performs the tree selection ceremony inside Tenju, where someone receives either a second or third-generation tree depending on whether or not a tree transports someone to them, and getting transported is far less common than not. Azusa gets transported but finds none of the second-generation trees are calling to him. The Emperor realizes what's happening, and Mitsuki guides Azusa to the room of First-Generation Trees, yet the head of House Tatsuki notes there weren't any trees there that chose him.
Inside the room of First-Generation Trees, Mitsuki leads Azusa down a path ending at one tree, which Mitsuki says is hers. She wants Azusa to name it and take it for himself, but while Azusa doesn't understand what she's saying, she suddenly buckles to her knees. Seeing Mitsuki's pale face makes Azusa realize that she is dying, and he sets her against the base of her tree.
Mitsuki tells Azusa that she is the reason that his mother wasn't allowed back to Jurai. As she says, Shuzan's story about her was a lie. The truth was that her father was an intelligence operative for a pirate guild hostile to Jurai who used her ability to gain information. One day, pirates attacked and almost annihilated the fleet carrying a head of state of a country friendly to Jurai, as they knew about their secret route to Jurai through Mitsuki. Such a scandal should've meant deportation, but Mitsuki reveals she can only survive with the power of all five of Jurai's First-Generation Royal Trees. The man who saved the foreign head of state knew about her condition and took it upon himself to assume all of the blame for the incident and was banished; that man was the older brother of Azusa's mother.
Azusa, now crying, doesn't want Mitsuki to blame herself for anything, but Mitsuki tells him that she was glad that she met him and asks if he will accept her tree. Azusa says that he can't hear the tree, but he realizes that Mitsuki's right eye is a prosthetic made of Royal Tree amber, and that she has been watching and hearing him since he arrived on Jurai. Mitsuki asks that Azusa take her with him to the outside world and tells him that she loves him just as she dies.
A mournful Azusa holds Mitsuki for some time, but he accepts her last request and takes her inside the hollow of her tree, laying her inside a pool of crystallized sap. He emerges from Tenju and decides to name his Royal Tree after the folk tale that Mitsuki told him about—the moon's fog seal, or Kirito. At that moment, he begins hearing Mitsuki, now Kirito's, voice ring out inside him.
Azusa finishes telling his story to Funaho and says that he was too young and immature to save Mitsuki, but Funaho cheers him up by saying that Mitsuki was glad to meet him. Jijii soon finds them, and after Funaho reunites with her grandfather, Azusa tells them he must visit somewhere. In truth, Azusa returns to Kirito and tells Jijii about the voice he heard while imprisoned by the Shank pirates. They find out the voice came from a spaceship that had crashed on the moon, and when they get up close to it, they discover it belonged to Masaki, the sister of the First Emperor of Jurai. Azusa explores the inside of the ship and discovers a small tree that reacts to the glow of his Master Key and projects an Astral copy—a reproduction of one's body, memories, spirit, and astral body—of Masaki. He meets and speaks to Masaki, who is disappointed Jurai didn't send additional research vessels to accept her registration of Earth. She proceeds to talk to him and Jijii for five days straight about incredibly common and low-brow topics before they excuse themselves back to Earth.
To summarize Masaki's tale, she was one of the scouts that scoured the Galaxy during Jurai's foundational period, and she had escaped from her "nosy and watchful parents and brother". Through pure luck, she discovered Earth and fell in love with it, choosing to spend the rest of her life there. Before she landed, she left her astral copy on the moon and filled out the planet's colony registration. Azusa offers to take Masaki back to Jurai, but she wants to remain on the moon and gaze upon Earth longer.
When Azusa returns to Kirito, Jijii informs him that the current Emperor of Jurai is ill and close to death, and they must return to Jurai immediately to ensure Azusa's succession. However, Azusa can't bear to leave without saying goodbye to Funaho, and he goes down to the village again. Azusa tells Asumi that he must return home because his "grandfather" is dying, but Funaho suddenly runs off. With Jijii demanding that he returns to Kirito. Azusa decides to bid farewell to Asumi and leave then and there, but Funaho returns to him with a basket of persimmons, chestnuts, and mushrooms for his grandfather. Feeling that Funaho's rustic simplicity and kindness have woven their way into his heart, Azusa suddenly scoops Funaho into his arms and asks if she'll come to Jurai with him. As Asumi expected, Funaho happily accepts, but before she leaves, she sees her younger sister and father one last time and gives them Azusa's comb to remember her by.
The Emperor of Jurai passes away just a few days after Azusa returns home with Funaho. However, during the mourning period before the new emperor's ascendence, controversy emerges over Azusa's insistence that Funaho, not his fianceé Misaki, be the First Empress. Misaki's father, Utsutsumi, confronts Azusa several times about this, but he is frustrated that talking to him is like talking to a brick wall. Lady Seto, his wife, doesn't share his frustration. In fact, she adores how Azusa keeps butting heads with Utsusumi.
Meanwhile, Shuzen Amaki, whose ambition to become the new Emperor ended when Azusa obtained a First-Generation Royal Tree, is delighted with how Funaho's presence has sewn discord. As the keeper to the gates to the Room of the Royal Trees, Shuzan has forbidden Funaho's entry because she isn't a member of the Imperial Family—a consequence of her unresolved status as First or Second Empress. He plans to have Azusa assume considerable psychological pressure from personally needing to guarantee Funaho's status and his loss of political power due to feuding with House Kamiki.
Utsutsumi and Seto go to the antechamber of their four-year-old daughter Misaki, but she has again outwitted her nannies and escaped. Meanwhile, Funaho is crying in her room, as she's suffering from a combination of culture shock, not being able to see Azusa for the moment, growing criticism toward her, and extreme homesickness. Suddenly, Misaki appears in her room and asks her what's wrong. They introduce themselves to each other, though Misaki mistakenly believes that both of them will be Azusa's First Empress. A few minutes later, Seto finds Misaki in the room, and all three of them start laughing when Funaho tells Seto that Misaki had entered her room through the window like a monkey.
That was the first time Funaho had felt at ease since coming to Jurai, and from then on, Misaki would keep visiting her, and they eventually become friends, though it does little to help with the stalled negotiations between Azusa and Utsusumi. Later, there is an attempt to assassinate Funaho with food poisoned with a nano-robot, but thankfully, Funaho's ahead-of-schedule bio-enhancement saves her, and it becomes apparent that the attempt on her life was an inside job. In response to Funaho's growing concern, Seto arranges for Misaki to live with Funaho to combine their studies, thus giving both of them full House Kamiki protection.
One day, both of them begin hearing something call to them and walk toward the source. They find themselves in front of the entrance to the Room of Royal Trees but are stopped by Shuzan, who doesn't believe their claim that they were led here. However, Seto and Azusa suddenly introduce themselves and interject that there have been cases of people being summoned to the Royal Trees outside of the formal ceremonies. Shuzan tries stopping them, but with the Trees themselves opening the gates, there's nothing he can do.
Inside Tenju, Funaho and Misaki, accompanied by Seto, Azusa, and Kotono of House Tatsuki as witnesses, enter the Room of the Second-Generation Trees. Eventually, they find the tree that was calling to them, but it turns out to be twin trees that have grown together. Being twins, they were more powerful than even a First-Generation Tree.
Her partnering with a Second-Generation Tree, in addition to newly revealed genetic data that shows she's directly descended from Masaki, the sister of the First Emperor, allows Funaho to quickly be accepted as First Empress of Jurai. As soon as the mourning period was over, Azusa becomes the new Emperor of Jurai, though his relationship with Utsusumi would remain awkward. Six years later, at the age of twenty, Funaho would marry Azusa. Fours years after that, she would give birth to her son Yosho, finally cementing her status and popularity with the people.
Five years later, Misaki, at the age of nineteen, would marry Azusa. Three years after that, the eight-year-old Yosho would select a First-Generation tree and name it after his mother, Funaho. Around the same time, Misaki gave birth to her first daughter, Ayeka. Four years later, with Azusa accepting Funaho and Misaki's wish that their children marry each other, Ayeka would be engaged to Yosho in a ceremony. It was a decision made without consulting the children, but Ayeka was ecstatic about marrying her half-brother.
Sasami—Misaki's second daughter—would be born seven years later. However, the time of destiny came just three years later. Seven hundred years before Tenchi Masaki was born, the space pirate Ryoko and her spaceship Ryo-Ohki would attack Jurai.
Just as she said, Seto came to see Azusa whenever her time allowed, and it was not to persuade him, but to watch Azusa pout. And Azusa would see her laughing and pout even more. There were even signs Seto was making him angry on purpose. 
- Kuroda and Kajishima, 1997. Page 66.