Throughout much of the series, her plans remain in shadow, and all the viewer sees of her much of the time is her watching a group of floating crystals which represent the Masaki Family, while commenting on the events of the episodes. She has three henchmen: Hotsuma, Tsugaru, and Matori, who do almost all of her work for her.
The tomb was launched, set to drift in the most remote parts of space. Somehow, it crashed on Earth and was buried, until an earthquake broke it open 3,500 years later. Yugi was released, but she was now a much different person than the innocent child from millennia before. She had become dark and warped, deciding to use her powers to change the earth into a world of her own.
Her plan changed when she met Sasami. Yugi created another new persona, this one the same as the young girl she once was. This Yugi would play with Sasami, who was the only true friend she ever knew. When Yugi attacked the Masaki shrine, her other side went off playing with Sasami so she didn't have to see the slaughter, which led to Yugi not having the energy to win the battle.
As her plan nears its end, she meets with Sasami, and the two play once more. She asks Sasami to come with her to her home, but Sasami says no, telling Yugi that they're just little girls, and much too young to live on their own. Yugi becomes angry at this rejection, and disappears, a sight which frightens Sasami. Sasami tells her sister Ayeka what happened to her friend Yugi, and Ayeka recognizes the name as the name of the one who attacked the Masaki shrine.
Yugi tells Sasami that she is making a world just for them, and, her voice breaking, asks her to join her. Sasami remembers their first meeting, and asks how Yugi could have done such atrocities, rejecting her proposal. Matori tells her to kill them all, but is herself destroyed by the brokenhearted Yugi. In a fit of rage Yugi declares she doesn't need friends or anyone, and puts an end to all of existence with the exception of Tenchi and the girls, who were protected by Ayeka's shield, before withdrawing into her inner sanctum.
Tenchi reunites the crystals and forms his sword, going after Yugi. A panicked Yugi screams that she doesn't want to be buried again and begins sending creatures to stop him, but Ryoko, Ayeka, Mihoshi, and Kiyone take out the guards, along with the other obstacles put in Tenchi's way. He makes it to the inner sanctum, finding himself in the room where Yugi spent much of the series. He finds a crying Yugi charging an attack, begging for Tenchi to leave her alone, and not lock her back up in the dark. Tenchi slices her attack in half, and Yugi begins screaming hysterically, which can be heard by all the others.
Suddenly, she is brought back to reality as Tenchi, who having dropped the sword, grabs her and slaps her. He gently lets her down, as her spiked armor falls from her. The two embrace and Yugi, crying, tells him of her fears of being alone. Tenchi tells her that all she needed was to come to the Masaki house, and she'd never worry about being alone again. As he comforts her, her world slips away, and all returns to normal.
Yugi chooses to be put into a sleep until she grows up and can control her powers better. She is put in the cave near the Masaki Shrine, and Sasami visits her every evening, telling her the events of the day. Ryoko hypothesises in the end that, since Sakuya was a reflection of Yugi, Yugi will grow up to be Sakuya, creating a bit more competition for Tenchi's affection.