Tenchi Muyo GXP tells the story of Seina Yamada, a young Japanese high school student with a supernatural penchant for bad luck living with his parents and younger sister in rural Okayama, Japan. One morning, following a hapless bike ride through the country, a large spacecraft crashes into the lake behind the Masaki residence, causing a violent tsunami that Seina is unable to escape from and he sinks, almost drowning. He regains consciousness shortly after, meeting Amane Kaunaq, the spacecraft's pilot, who gives Seina an application. Seina takes it, and shows it to his family at home. Mistaking it for a contest entry, his mother and sister aggressively force him to fill it out; afterwards he retreats to his room and falls asleep. The following morning, awakened aboard a vessel in orbit, Seina is informed by an official that he has successfully joined the Galaxy Police. At first, Seina wanted to leave and return home, but when he saw where he was, he changed his mind.
After being recruited, Seina soon found himself involved in a high speed chase away from space pirates who wanted to loot the transport ship until they were all captured by Lady Seto Kamiki Jurai. She warns Seina that cadets of Earth origins are not accepted and must find a way to prove himself worthy of being a GXP cadet or be sent back without any memories of the encounter. Seina later encounters Ryoko Balta, a space pirate, who wants him on her side. After Seina’s ordeal, he and the others arrived at GP headquarters to get Seina enrolled. While he was away, Seina continued to think about his childhood friend and crush, Kiriko Masaki.
In the G.P.'s immigration department, Seina learned that Kiriko worked for the GP and her work with them was a secret from even her brother Kai. Immediately, she pleaded to the boy without success for him to leave. Soon afterward, she was assigned to the G.P. Academy, along with Amane Kaunaq mainly to keep an eye on Seina, since he already made a name for himself by capturing the most pirates in GP history. During that time, Seina, along with Airi Masaki (Tenchi’s “grandmother”) learned more the GP and met Erma and Seiryō Tennan, a teacher who was once engaged to Ayeka until his defeat, now he has a hatred for humans and takes his hatred out on Seina. After getting all the paperwork finished, Seina was fully erolled and so his adventure begun.
One part of his training was to go through body enhancement, which meant that his body would be hard for him to use until he learned how to move right without flying across the room. After Seina would receive the body enhancing modifications he needed to keep up with the other students, Seina moved into Amane's private home, along with Kiriko and Erma. Then Seina gets commissioned on his first assignment as a GP Academy cadet when he gets into a cargo mission after getting his body enhancement problems under control. His mission ends when space pirates under the command of Kyo Komachi attack the GP-led cargo ship with Seiryo being kidnapped. His bad luck case gets him into trouble when Tarant Shank, a notorious space pirate, encounters the young cadet and decides to eliminate him.
When Seina's bad luck was found to have an effect of attracting space pirates, the GP capitalized on it by placing Seina in command of one of the Decoy Fleet's newest ships, the Kamidake along with Amane and Kiriko. After finding and capturing pirates, Seina and the rest of the GP crew he was embedded with gets their first pay check. He does a little errand for NB, the surveillance robot who Amane had tampered with during his training with Amane. Meanwhile, the Pirate Council of the Daluma pirate guild decides that Seina is too dangerous to exist and orders his termination. They order Ryoko Balta to use her spy Erma to do the job. Erma accompanied Seina on a shopping trip at the G.P. Academy. But when she finally confronted Seina, the boy gave her a present - a simple star pendant. Overcome with guilt and shame, Erma then begun to change. She turned out to be a disguise Ryoko and confessed to Seina. She then turned the gun she planned to use to kill Seina on herself. But before she could pull the trigger, Amane Kaunaq and Kiriko Masaki, who were jealous because they each fell in love with Seina, barged in and Seina stopped her. Ryoko was later captured by Airi; it seemed that a short time ago, Airi found out that Erma was really Ryoko but didn't have the evidence to prove it.
During a mission to deliver a package to Lady Seto , Seina’s ship was badly damaged and was in trouble until Ryoko was released from prison and was given an offer to join Seina’s crew which she accepts. Once on Jurai, the girls and Seina learned that the package was a second-generation Juraian tree-seed, which the Daluma Guild had procured in the hopes of discovering its secrets. With his ship damaged beyond repair, Seto presented Seina with a ship designed by Washu Hakubi, which was named the Kamidake II by Seina. The ship consists of the main ship body and a cabbit, similar to Ryo-Ohki, named Fuku by Seina. Fuku differs from Ryo-Ohki in that Fuku serves as a terminal body and more importantly, the power source for the ship, thus is not able to transform into a ship. Seto also tasks Seina an escort mission with a girl named Neju to GP headquarters. Neju Na Melmas may look young, but is a 3000 year-old high priestess and spiritual leader of her planet. She took an instant liking to Seina like a big brother, which soon turn to love.
During the time Seina commanded the Kamidake and Kamidake II, he was earning an equivalent to a fleet commander's salary. However, because he was still a cadet, that money was kept in a special account until he graduated and was given what he would normally earn. The interest the money accumulated, however, was forwarded to his family on Earth. It was so much money that the Yamada family used it to build a huge new home, as well as building a huge supermarket in place of their small grocery. While Seina was visiting Tenchi back on Earth, Amane, Kiriko, Ryoko Balta, and Neju, who was visiting at the time, worked at the Yamada's supermarket, where they were worked until exhausted.
After their visit on Earth, the crew learned that Seiryo joined the Daluma pirate guild with his own “Good Luck Fleet” with a plan to defeat Seina for good. In order to defeat Seiryo at his own game, Airi and Lady Seto organize a match between the two GP officers which Seina won. After Seiryo and the Daluma guild was captured, Seina's squad gets disbanded and renegade officials of the GP Army gets interested with Seina's ship. Seina's crew gets arrested by GP soldiers for plans to hijack their own ship while Seina gets stranded on an unknown planet with a familiar enemy. Being taken in by a village, Seina assists them to defeat Tarant's pirate guild when he discovers an ancient mech on the planet. In the end, Tarant was defeated again and the renegade officials were arrested for treason.
Seina and the others part ways as Seina is about to graduate with the rest of his batch. Afterward, it was revealed by Emperor Azusa and Empresses Funaho and Misaki that the mecha (now known as Idol) had as its power source a first generation Jurai tree seed, with the seed bonding itself with Seina. As a result, Seina is now third-in-line to the Jurai throne, behind Yosho and Tenchi. Thus, a political marriage between Seina, Amane, Kiriko, Ryoko Balta, and Neju was arranged for political reasons. Seina is initially very disposed against what he thinks is an attempt to force the girls into marrying him, but is later persuaded that they are doing so out of their own free wills. Tarant returns to try and eliminate him for good. Luckily, Shank's impaitence gets the best of him and Seina was able to subdue him. Later on, Seina gets kidnapped by some of Lady Seto's court ladies who were actually agents of the Renza Federation seeking to use Seina's abilities to rid their home from marauding pirates, kidnapped Seina into their small ship, and began to molest him in a public broadcast to ensure the Renza Alliance's political bond with the Jurai Royal Family. As a result, the four are included into the marriageas well as the crew of the Kamidake. All the girls were last seen in the Renza territory searching for some pirates under the command of their captain and husband Seina Yamada.