In a dark chamber at the centre of Galaxy Police headquarters, the lock on a subspace containment field fails. A dark shape emerges, and a wave of energy engulfs GPHQ, sucking it out of existence. In a flash, the entire space station vanishes, then reappears moments later, nothing more than burnt-out wreckage. The last communication is an emergency broadcast; Kain has escaped. The dark shape heads for Earth and descends into the atmosphere. In Okayama, the effects of this event are already being felt; Tenchi Masaki is beginning to disappear...

Some time later, Tenchi's brief but unsettling experience is behind him. He is showing Ryoko, Ayeka and Sasami some old home movies that his dad made. The film they are watching is of his mother, Achika, as a high-school student. As they watch, Achika's image vanishes from the screen, and Tenchi himself starts to fade from existence again. Fortunately, Washu was quick enough to spot the impending disaster and erected a force-field just in time to save him. She explains that she has detected an anomaly in the space-time continuum centred on the Masaki family 26 years previously. Some event in the past has affected Tenchi's mother, wiping out Tenchi and even the Masaki shrine. They have no choice but to travel back in time to when the anomaly occurred and set history straight again, and Washu uses her time cause/effect controller to send them all back to 1970.

Following their arrival, the girls carefully integrate themselves into the high-school where Tenchi's mother is studying so they can keep a close watch on her. Ayeka and Ryoko pose as transfer students, Kiyone works as a janitor and Mihoshi as a teacher. Tenchi is under Washu's orders to stay out of sight, for fear of causing further temporal anomalies if his parents should see him. It isn't long before Ryoko spots a strange young man in the school who seems to be watching them with interest.

After returning from school that evening, Achika is surprised to find her two new classmates, Ryoko and Ayeka, staying at her house. With the aid of a mind-control spray invented by Washu, they have managed to persuade Katsuhito to allow them to stay, meaning they can keep a close eye on Achika at home too.

Later that evening, Washu makes contact with the group through her communication equipment in Sasami's backpack. She warns that Achika's disappearance is due to occur some time within the next week. However, the shield that is protecting Tenchi is also due to run out in 7 days.

At school the next day, the group meet in a storage shed to discuss the problem. None of them have noticed anything particularly odd, so they still have no idea about what happens to Achika. Suddenly, Tenchi begins to disappear again. He collapses, wracked with pain as waves of energy coruscate across his body. The girls realise that no-one is watching Achika, and rush to find her. They search the school, only to find she has gone missing. They return to the shed to find Sasami has had to use the portable energy net in her backpack to save Tenchi from vanishing altogether.

Tenchi is safe, for now at least, but Achika is still missing. Fortunately, Ryo-Ohki picks up Achika's scent and leads the gang to where Achika and Nobuyuki are, out on a hill near the school. Nobuyuki is busy drawing, and Achika asks to see his work. He shows her the house he has drawn, identical to the familiar Masaki home back in the present. The girls soon arrive, and are relieved to see that Achika is perfectly all right and is getting along well with Nobuyuki. However, the strange young man Ryoko spied earlier is also watching them.

That night, Kiyone is taking a bath when she suddenly vanishes. She reappears in Washu's lab in the present day, having been brought back temporarily by Washu to hear some important news. She has found that the energy signature detected when GPHQ disappeared matches the one at the time of Achika's disappearance, so both events must have been caused by the same thing. Accessing the GP database aboard Kiyone's shuttle, Washu finds details of the class-A criminal Kain who was captured by the Galaxy Police 100 years previously. They realise that Kain must be the one responsible for Achika's disappearance, and that he is due to attack her some time within the next four days in Tokyo, where Achika's class is headed on a school trip!

In Tokyo, Tenchi and the girls book into the same hotel as the school trip party to stay near Achika. When the class visits a park in the city, Ryoko and Ayeka are delighted to see Achika and Nobuyuki are getting along so well. As Tenchi watches from afar, he begins to phase out of existence again, and Sasami has to rescue him once more with the portable net. Meanwhile, Ryoko spots the strange man again, and gives chase. However, he is fast - inhumanly fast - easily outpacing Ryoko, and she loses track of him.

The school trip takes them to the Nakamise shopping arcade, where Achika is approached by the strange man. Ryoko is soon on his tail again, and she chases him down one of the back streets. She has lost sight of him again when she feels a hand pressed into her back. The strange man has cornered her, and he warns her not to move. He reveals that he is a Galaxy Police special operative, who survived the destruction of GPHQ. He explains that Kain is seeking revenge on the Juraian royal family for helping the Galaxy Police to imprison him 100 years previously, and that he wants to destroy anyone who possesses Jurai energy, including Achika and Katsuhito. However, as a Galaxy Police operative he is also obliged to capture Ryoko, but is willing to leave her be until he destroys Kain.

That night, back at the hotel, Kiyone reappears from another brief trip to the present carrying more equipment from Washu. Communicating with the gang via a holographic projector (that resembles Yukinojo from the OVA series), Washu explains that only a huge amount of Jurai energy can suppress Kain, and even Katsuhito could not produce that much energy without endangering his life. However, she has a plan; using another of her inventions, the gang can harness spiritual energy from the five-colour Fudo shrines in Tokyo to generate enough Jurai energy to recapture Kain. As Washu finishes her explanation, Tenchi suffers another phasing-out attack. Sasami rushes to help Tenchi with the energy net again, but he asks her not to, explaining that he needs to be able to cope with the pain of his disappearance attacks if he is to stand any chance against Kain. As the attack subsides, Ayeka rushes into the room bringing news that Achika has collapsed. Fortunately, she is all right, and is only suffering from anaemia. Ryoko wonders if Kain's influence is responsible for Achika suddenly falling ill, and Kiyone agrees; Washu has told her that Kain will definitely attack Achika the following day during the class visit to Tokyo Tower.

Tomorrow arrives, and the girls each set out separately to the shrines of the five-colour Fudo, and Tenchi follows Achika to Tokyo Tower, taking the energy receiver. With the power boosters in place, the gang is ready for Kain's appearance. Right on cue, a storm breaks over the tower, and Kain appears. He blasts a hole in the side of the elevator shaft and locates Achika. As he advances towards her, he is struck from above by a hail of laser blasts. The Galaxy Police operative has tracked him down, and was waiting on the observation deck to ambush him. With Kain distracted, Tenchi takes the opportunity to try and lead his parents to safety. On the deck above, Kain attacks the GP operative and, being far too powerful for one man to defeat, simply rips him apart. Meanwhile, Tenchi leads Achika and Nobuyuki onto another floor of the tower and puts the Jurai energy receiver in position. Kain appears and Tenchi confronts him, drawing Tenchi-ken (the sword given to him in Tenchi Universe episode 23) to attack him. Tenchi is on the brink of being destroyed by Kain when Achika turns and orders him to stop. Kain turns his attention on Achika, the strongest source of Jurai energy. Tenchi staggers to his feet and shouts to Nobuyuki to switch on the energy receiver. Washu's invention works perfectly, and bolts of energy leap from the Fudo shrines to Tokyo Tower. The receiver activates and starts sucking Kain into subspace. However, Kain grabs hold of Achika to drag her in with him. Nobuyuki tries to hold her back, but they are both drawn into subspace along with Kain.

With Nobuyuki and Achika gone, Tenchi is in despair. However, Washu has a solution; a tough decision, but their last hope to save Tenchi's parents. Using a brain wave transfer helmet, Tenchi's mind can be linked to Achika's, then Ryoko can teleport them all to the location seen through Achika's eyes, allowing them to fight Kain hand-to-hand. Since Kain is far too powerful for any of them to defeat unaided, Washu sends the dimensional cannon, a weapon so destructive it can wipe out an entire galaxy.

Meanwhile, on a desolate windswept landscape in subspace, Nobuyuki regains consciousness. He rushes to find Achika, who is lying unconscious on the ground. As he reaches her, Kain appears and seizes them both.

Ryoko, Ayeka and Tenchi change into their battle outfits, and Kiyone prepares the dimensional cannon. With the transfer helmet on, Tenchi sees the scene through his mother's eyes just as she comes to.

Kain is dangling Nobuyuki helplessly in the air in front of Achika. He hurls him brutally to the ground. The distressed Achika wrestles herself free of Kain's grasp and runs to Nobuyuki's aid. She turns to face Kain, and mutters that she can never forgive him for trying to hurt Nobuyuki. Kain watches in disbelief as Achika's tattered school uniform is replaced by flowing Juraian robes. Knowing he cannot defeat Achika in her Juraian guise, Kain changes strategy, and he opens a massive void in his body, threatening to absorb Nobuyuki and Achika. They are moments away from being sucked in when Tenchi, Ayeka and Ryoko arrive. Tenchi slashes Kain's face with his sword, and Ryoko snatches Nobuyuki and Achika away from the void. The wounded Kain changes form, shedding his humanoid mask and becoming a massive beast with hideous fangs. Tenchi attacks with his sword again, but Kain is far too strong for him, and he is sent flying. Kain engulfs everyone in powerful energy bolts, but Achika resists the pain and picks up Tenchi's sword. In response to Achika's powerful Juraian energy, the sword grows, its blade of light several times longer than before, and it absorbs Kain's energy attack. She stabs the blade right through Kain's body, then slices his arm off. As Kain roars with pain, she brings the sword down in a final blow, splitting him in two, and his monstrous form boils away into nothing.

A portal back to Tokyo appears, and the girls step through, carrying Tenchi and Nobuyuki. As Achika reaches the exit, she is jerked back by something grabbing her hair; Kain's twisted remains have reanimated, still determined to kill her! Kiyone fires the dimensional cannon, and Achika manages to break free as the blast hits. Kain evaporates with a final anguished scream.

The battle over, the girls say farewell to Achika. Ayeka has one last task to perform; erasing Achika and Nobuyuki's memories of Kain's attack. Achika thanks them for their help, and they disappear back to the present.

After her encounter with Kain, Achika lost her Jurai powers, which, Tenchi surmises, may have lead to her premature death, but he takes consolation in the fact that his parents were still able to spend a few short but happy years together. In 1979, Achika gave birth to a healthy baby boy, whom they named Tenchi.

Back in the present day, Tenchi and the girls return to normal life in the house that Nobuyuki and Achika made. History is set straight, and all is well once more.