Many years ago, a human and his partner Gardevoir entered a sacred dungeon, greedy of the rare Pokemon living in it. They encountered Ninetales, and the trainer grabbed one of its tails. Ninetales cast a curse on that human, but Gardevoir sacrificed herself and absorbed his curse. Ninetales asked the human if he wants to save Gardevoir, but he had already fled. Ninetales than said that the human shall turn into a Pokemon one day, and will make the balance of the world upset, bringing many natural disasters. Gengar is the human in the curse - the one in the Legend of Ninetales.
He first entered as the leader of team Meanies, stealing the player's mail inside his/her mailbox. Luckily, Pelipper delivered more mails then.
Then he appeared with the other team members of Team Meanies, attempting to go rescue Metapod instead of the player's team, saying they will force Caterpie to join their team. At the deepest part of the Sinister Woods, they appeared again as the bosses.Gengar then overheard the conversation between the player and Xatu, and convinced the Pokemon in the Pokemon Square to chase the player and her/his partner out, saying that the player is the human in the Legend of Ninetales.
While the player is on the run, Gengar is the Pokemon that doesn't do anything with his team, saying he is only going to receive information from other rescue teams. When he saw the player being back and confirmed that s/he is not the human in the Ninetales Legend, he and Team Meanies were chased out instead.
Gengar also gave a Nightmare to the player afterwards, but fled away crying when he saw Gardevoir, his partner when he was still a human. He also helped with making the Teleport Gem.
After Rayquaza destroyed the falling star and the player ended up in the netherworld because of the aftermath of the explosion, he attempts to drag the player into the world of darkness, but had forgotten the path, so he decided to dump the player alone there, but he later went back and saved the player afterwards, likely because Gardevoir had appeared in her/his dreams. He also saved the player's partner and team members.
After the credits rolled, Gengar asks the player to escort him onto the peak of Mt. Freeze, revealing that he is the human that fled in the Ninetales Legend and is the trainer of Gardevoir. Ninetales gave him the Nine Tail Crest, sending him to Murky Cave.
At the deepest floor of Murky Cave, Gardevoir is revived and released from the curse, but had lost every memory about Gengar. She asks who Gengar is, and Gengar replied sadly: 'The name is Gengar.' He is not seen again then.