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The Passage of Time is located in Deep Dusk Forest in Explorers of Time, Darkness, and Sky. The Passage of Time is used to take long distance trips, such as trips to the past, according to Celebi. Another Passage of Time is found at the pinnacle of Vast Ice Mountain in the final Special Episode.
After the player and their partner are trapped in the future with Grovyle, they make their way to Celebi, who informs them that the only way to get back to the present, is to take the Passage of Time, located in Deep Dusk Forest. It was when the team made it to the Passage of Time that they were trapped by Dusknoir and the player's past was revealed. Dusknoir's master, Primal Dialga interfered with the time traveling, but Celebi was able to time travel them closer to it. The player, their partner, and Grovyle were able to make it back to the past by jumping into it.
In the Special Episode In the Future of Darkness, Primal Dialga is driven berserk by history changing. By instinct, he locates the second Passage of Time and heads towards Vast Ice Mountain to destroy it. It is not revealed what would happen if the Passage of Time were damaged; even Dusknoir does not know, but he recognizes that it would be very dangerous. At the pinnacle, Grovyle, Dusknoir, and Celebi finally confront Primal Dialga. They manage to defeat him before he destroys the Passage of Time.