Pokémon Mystery Dungeon: Gates to Infinity
Hydreigon was first seen in a vision chasing down Munna, and was described as an evil Pokémon who is pure destruction in Pokémon form, devours everything in his path, and said to be the cause of the world's balance being disrupted. In truth, Munna's story about him was all a lie to trick the player, and Hydreigon is actually the physical avatar of the Voice of Life, the form of the world's will to live, who called upon humans to save the Pokémon world as no Pokémon could hope to save it. He originally first contacted the player in a dream before Munna intercepted it. By using Hydreigon's voice, Munna tricked the player into thinking Hydreigon was evil.
When the player was cornered by Toxicroak, Salamence, and a portion of Munna's gang, Hydreigon saved the player and whisked them to safety. It was only when they stopped to rest that Hydreigon explained everything to the player. He explained that he is the Voice of Life and had contacted many other humans who had heard his plea to save the Pokémon world since normal Pokémon can't get close to an entity responsible for the world's balance being disrupted, the Bittercold. When the other humans were defeated by Munna and her gang and sent back to the human world, Hydreigon pleaded to the player, who was the only human left, to save the Pokémon world.
After rescuing the player's partner from Munna and her gang, Hydreigon led them through the Scorching Desert to make it to the safety of Post Town. However they were ambushed by Kyurem, who froze Hydreigon solid and destroyed his physical form. Despite not being with the player and their partner, Hydreigon, being the Voice of Life, was able to lead the players` friends to their location after the player became seriously injured by Kyurem.
After the Bittercold has been defeated, Hydreigon will have retained his physical form once again, and thank everyone for combining their efforts in saving the world. Later, as the Post Town celebrates the achieved victory over the Bittercold, the player goes up on the hill to get a break from the excitement, meeting up with Hydreigon, who tells the player that they have to leave the Pokémon world, since a long-run presence of a human in the Pokémon world would cause a distortion which would strain the very fabric of the universe itself. Hydreigon also tells the player, that once they leave the Pokémon world, everybody would forget that they had ever been there. Hydreigon informs that the player that the departure will occur the next day, giving them time to tell about this to others. However, the player decides not to tell anyone, not wanting to ruin their fun at the celebration. The next morning, the player meets Hydreigon up at the hill again, and starts the departure from the Pokémon world with him, surrounded by a bright sphere of light. Before leaving the player to continue the departure on their own, Hydreigon gives the player a Frism, which contains a message from the player's partner and friends, who anticipated their departure, and a promise to never forget them.
During the post-game, Hydreigon joins the player's team, wanting to stay at the Paradise and help them out in their missions. After a while, Hydreigon gathers everybody together and tells them that the fact that they hadn't forgot the player has proven that their will has been strong enough to prevent these certain laws of nature, once considered by him to be unchangable, from occurring. This also seems to have made it possible that the player might, after all, have a chance of returning to the Pokémon world. Hydreigon tells them that at a dungeon known as the Worldcore, there exists a place called the Hill of Universal Order, where one can make a wish, and, if it can be fulfilled without disturbing the balance of the universe, will be granted. The player's partner decides to go there, wishing for the player to return and be able to travel between the two worlds. After the player's partner has made it through the Worldcore, Hydreigon will be waiting for them at the Hill of Universal Order. The partner makes their wish for the player's return, but the wish seems to be too difficult to be granted, causing the cave to start collapsing. Despite of this, the partner won't give up, and refuses to leave. Hydreigon then calls to the player, telling the player that if their will is strong enough, they would be able to return.
After the player has returned, Hydreigon will stay at the Paradise, being ready to join the player and their partner in any possible request mission.
Pokémon Super Mystery Dungeon
Like many other Pokémon from the previous Pokémon Mystery Dungeon games, Hydreigon reappears in Pokémon Super Mystery Dungeon. He first connects with the player at the end of a dungeon via a "Meet Up" mission. Afterwards, he will randomly appear in the various towns. If talked to, he will recognize the player, but is dismayed when the player doesn't remember him.