Set a week after the conclusion of the second Tenchi Muyo! Ryo-Ohki OVA series, with Emperor Azusa making his daily visits to the Masaki household on Earth, the True Tenchi Muyo! light novel trilogy reaches back across centuries and millennia to explore the hidden history of the Tenchi Muyo! universe. Each volume uses a brief framing sequence in the present before delving into the distant past of a major character, revealing the events that shaped the Jurai Empire and led directly to the situation Tenchi finds himself in.

The first volume, Jurai, focuses on Azusa, the current Emperor of Jurai and father of Ayeka and Sasami. Long before he wore the crown, a young Azusa lived with his parents on a colony world until a pirate attack changed everything. Discovered by the formidable Lady Seto Kamiki, Azusa was brought to the planet Jurai and thrust into the complex and often dangerous world of Imperial politics. The novel follows his struggles to prove himself worthy of the Royal Trees, his rise through the ranks of Juraian nobility, and his fateful journey to Earth during Japan's feudal era. There, he encounters a young woman named Funaho and rescues her from bandits, setting in motion the chain of events that would lead to her becoming his first wife and the mother of Yosho. The story also shows his eventual meeting with Misaki, Ayeka and Sasami's mother, and his ascension to the throne.

The second volume, Yosho, turns to the mysterious past of Tenchi's grandfather, known on Earth as Katsuhito Masaki. Born as the son of Azusa and the Earth-born Funaho, Yosho faced prejudice among the Juraian nobility due to his mixed heritage. Seeking to escape his complicated feelings for his stepmother Misaki, the twelve-year-old prince enrolls in the prestigious Galaxy Academy, a massive institution the size of a solar system. There, he is assigned a student guide named Airi Magma, the daughter of a powerful religious leader from the planet Airai. As Yosho navigates the tense political and religious conflicts between Jurai and Airai, he grows close to Airi while also crossing paths with the brilliant but troubled scientist Washu and the sinister Kagato. The novel climaxes with Yosho pursuing the space pirate Ryoko across the galaxy, culminating in their battle over Earth. Unable to return home and choosing to guard Ryoko's sealed form, Yosho decides to remain on Earth, where he eventually starts the Masaki family line.

The third volume, Washu, reveals the origins of the self-proclaimed greatest scientific genius in the universe. Over twenty thousand years before Tenchi's birth, Washu lived as a goddess and was one of the three Choushin, the creator deities of the Tenchi Muyo! multiverse. The novel explores her time at the Imperial Science Academy after she chose to abandon her divine status and live as a mortal. It focuses on her deep friendship with a student named Naja Akara and her tumultuous relationship with Mikamo Kuramitsu, a man who would become her husband and the father of her child. The narrative details the circumstances that led to Washu's imprisonment by Kagato and, most significantly, reveals the true origins of the creations that would define her legacy: the space pirate Ryoko and the cabbit Ryo-Ohki, showing how they were born from both her scientific genius and her personal tragedies.