Many eons ago, after they had created the universe and its many dimensions, Tokimi and her sisters Tsunami and Washu were trying to figure out if it were possible to create something more powerful than themselves. While Washu and Tsunami had gone their separate ways to accomplish that end, Tokimi remained to carry out their original plan, by creating abnormalities in the universal fabric to create this superbeing. It was through her manipulations that Z had gained the power of the Lighthawk wings. But she also saw that Z was unstable and wondered if her sisters had better success. That was the reason why she wanted Clay to bring Washu. However, because Clay had ulterior motives in mind, she had D3 seal away Clay's memories of her involvement with him.
Later, when Z rebelled against Tokimi and tried to kill Tenchi, she had sought to contain her errant servant. But because of this, when Tenchi's powers threatened to destroy all universes, Tokimi and her reunited sisters tried to contain a possible explosion, but Tokimi was attacked by a being called the "counter-actor," thus putting the universe in danger. The "counter-actor" in a human form was revealed to be the Empress Misaki gone mad. Tenchi (or perhaps the personification of Tenchi's powers) later saved Tokimi from death by calming the rage of the "counter-actor".
Afterwards, Tokimi would be instrumental in discovering that a set of extra cells that Noike had was in fact the female half of Kagato. Also, Tokimi would reveal a child form, much like Washu uses, which she used during the final OVA episode. Tokimi was also a guest at the wedding of Nobuyuki and Rea Masaki, occupying the "resident kami" portion of the shrine.