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Primal Dialga sends Dusknoir to pursue Grovyle and the main characters. He pretends to be an explorer who is famous for his wisdom and solo explorations. At first, when Dusknoir meets the player, he does not know the player's name, and actually rescues the player and the partner from the Luxray clan (Manectric clan in Explorers of Sky). He portrays Grovyle as a criminal from the future, and says that he is also from the future to bring Grovyle to justice. The whole guild falls for Dusknoir's lie and goes after Grovyle, trying to prevent him from stealing any more Time Gears.
At one point, the player and partner approach Dusknoir with questions about the player's Dimensional Scream ability, and ask if he knows anything about where the player came from. They mention the player's name, with the player noticing that despite claiming to know nothing about the player's memory loss, Dusknoir might have had a small smile. When Grovyle is caught and is about to be taken back to the future, Dusknoir calls the duo up to him and says hastily that it is too soon for good-byes, grabbing them both and taking them to the future before the rest of the crowd even realizes what has just happened. However, they manage to escape from the future with Grovyle as their new ally.
They meet Dusknoir again at the end of the Hidden Land, battling him and six Sableye. He is finally defeated when the player, partner and Grovyle force back an attack, that appeared to be Shadow Ball, into the 'mouth' on his stomach, severely injuring him and sending his Sableye running back to the future in disbelief that Dusknoir had lost. After they defeat him, he rises and unleashes an attack on the player with the intent of finishing things, but Grovyle steps in. Grovyle then takes Dusknoir back to the future with him to prevent him from stopping the player and their partner from changing the future. Dusknoir, Grovyle, Primal Dialga, the Sableye, and the player are all erased from time when the player and their partner stop Temporal Tower's collapse, but Dialga revives the player as a reward for their sacrifice.
In Pokémon Mystery Dungeon: Explorers of Sky, Dusknoir, Grovyle, Primal Dialga and the Sableye appear to survive, but are trapped in the dark future. Primal Dialga orders for its army to execute Dusknoir for his failure in the past game, but Dusknoir gets away with the help of Grovyle. The two of them team up together to defeat Primal Dialga.
As they travel through the now-abandoned Temporal Tower and Dark Ice Mountain, Grovyle and Dusknoir begin to develop a sort of kinship with each other. Dusknoir eventually asks Grovyle why he is willing to sacrifice his life to change the past (hence eliminating the dark future from existence), and Grovyle responds that it is better to live a short life with glory than a long, empty life.
At the end of Icicle Forest, they see Celebi held hostage by a Spiritomb. Grovyle attempts to rescue her, whereupon he is captured in an electric field; Dusknoir reveals the supposed execution order was a ruse; he intends to possess Grovyle, travel to the past again, and ruin things there. However, Grovyle, speaking of his newly-formed trust in Dusknoir, believes that not everything was indeed faked, that Dusknoir did identify with Grovyle at some point during the journey. Grovyle is correct - Dusknoir had begun to question whether self-preservation in a bleak future was a good idea. Just before the electricity from the icicles Grovyle is captured can melt away his spirit, Dusknoir saves Grovyle by knocking him out of range. Spiritomb flees, and Primal Dialga jumps down, and, angry at Dusknoir, starts beating him up. The Sableye attempt to try and stop him, but are knocked away by Dialga's Roar of Time. Dusknoir is then saved by time starting to flow again, making Primal Dialga leave.
At this point, Primal Dialga appears and attacks Dusknoir for his betrayal. The effects of Dialga's defeat in the past (the final boss battle in the main storyline) begin to take effect; time is slowly starting to flow. Dusknoir, now sincerely sharing Grovyle's goal, teams up with he and Celebi in an effort to find Primal Dialga. After cornering Dialga at the Passage of Time, they defeat him, and the effects of the past finally take effect in full force; the Pokémon of the future are vanishing, and time flows again. After Primal Dialga vanishes, Dusknoir asks Grovyle one final question: whether this sacrifice is worth his life. With Grovyle's assurance that it is, he finally feels content and vanishes; Grovyle and Celebi follow soon after. Soon, everything in the future is erased from time.
However, the Pokémon of the future (Dusknoir, Grovyle, Celebi, Dialga) eventually find themselves in a newly-restored future, appearing at the Passage of Time, surprised they have not vanished. Dialga, now restored to his normal state, remarks that their resurrection is due to the actions of a being "on an even higher tier than itself." With joy and hope restored to the future world, each of them is free to live their life as they truly wish.
