Celebi is seen in the future, where she originally helped Grovyle escape to the present to collect Time Gears. Celebi can travel short distances through time all by herself, but for big trips of many generations, she uses the Passage of Time at the end of Deep Dusk Forest. She does not like the everlasting darkness of the future, and is willing to sacrifice herself to get rid of the planet's paralysis.
When the player and partner are trapped in the future with Grovyle, Celebi guides them, by joining their team, through Deep Dusk Forest to the Passage of Time, where they can escape to the present again. When they make it there they are cut off by Dusknoir and his Sableye, as well as Primal Dialga. Primal Dialga interferes with Celebi's time traveling, but thanks to the partner's quick thinking, she is able to teleport them forwards in time just past Dusknoir and his Sableye and close enough to the Passage of Time to escape. She repeatedly claims it's impossible for Dusknoir to catch her and this seems to hold true, as it appears she escapes Dusknoir after helping the player, partner, and Grovyle go back in time.
In Pokémon Mystery Dungeon: Explorers of Sky, Celebi reappears as a prisoner of Spiritomb at the end of the Icicle Forest, used by Dusknoir to bait Grovyle into standing in between the four electricity-generating pillars of ice to literally melt away Grovyle's spirit. Dusknoir would then occupy Grovyle's body and return to the past; however, he gives up on the ploy right as Grovyle's spirit was almost completely melted away. Out of nowhere, Primal Dialga then appears, and attacks everyone except Celebi and Spiritomb; however, it is after this time that the long-paralyzed planet finally starts moving again, as pointed out by Celebi by breezing winds and, most notably, an aurora. After being saved by Grovyle and Dusknoir, they chase the berserk Primal Dialga to the top of Vast Ice Mountain, where she helps in the successful effort to take it down. Afterwards, she, Grovyle, Dusknoir, Sableye, Dialga, and the other Pokémon of the future are spared of being erased from history, presumably by Arceus.
She reappears as a character that needs to be rescued in Super Mystery Dungeon through Grovyle's request. Rescuing Celebi will allow her and Grovyle to be used as playable characters.
Apparently, Celebi has feelings for Grovyle, which are shown when the player and the partner are trapped in the future, even blushing when the player talks to her. Right before they both vanish in the morning sun after defeating Primal Dialga at the Vast Ice Mountain Peak, Grovyle holds Celebi in his arms as they watch the future's first sunrise, with Celebi commenting that she had never seen such a beautiful sight before.