Team Meanies get their introduction in the games when they confront the player's team and steal their mail; they explain that they only became a rescue team for the wealth and power it gives them and that they hope for world domination. Fortunately for the player, just after they leave, Pelipper delivers some new mail. At this point, the player's team and Team Meanies become rivals.
The next encounter with Team Meanies is just after the player is given a mission to rescue Metapod. Team Meanies challenge the player to try to save Metapod first; if they succeed, they will force Caterpie to join them. The player must later confront them in the Sinister Woods, where they are defeated in battle just before retrieving Metapod.
Further in the game, Gengar eavesdrops on the player, partner, and Xatu at the Hill of the Ancients, learning of the player's possible involvement in the Ninetales legend. Following this, Gengar spreads untrue rumors about how the player is the cause of all the natural disasters and must be destroyed to save the world, causing the residents of Pokémon Square to heavyheartedly run the player and partner out of town.
As everyone tries to hunt down the player (most of them giving up at Mt. Blaze), Gengar remains in Pokémon Square, having assigned himself the role of gathering intelligence on the situation. He later learns from a panicked Medicham that the player and partner have met with Ninetales at Mt. Freeze and returned to Pokémon Square. Gengar tries to protect his rumors by pressing the player and partner for hard evidence, but Pelipper delivers proof in the form of newspapers to the Square, stating that they indeed met Ninetales under Team A.C.T.'s watch and that the player is not the human from the Ninetales legend, proving Gengar's rumors to be malicious lies. After Lombre reads this out loud, he, Snubbull, and Shiftry angrily chase Team Meanies out of Pokémon Square.
Gengar later arrives at the square following the defeat of Blastoise, Octillery, and Golem in Magma Cavern and begins mocking all the rescue teams present at the gathering for attempting against such odds. His words spread fear, doubt, and uncertainty before the partner speaks up against this and successfully encourages everyone, stating the team's intent to enter the dungeon and rescue Team A.C.T. Foiled and once more embarrassed in the middle of the square by the player's team, Gengar angrily leaves.
A few nights later, Gengar uses Dream Eater to see into the player's dream in an attempt to find some dark secrets within the player and thus expose them for who they really are, remarking to himself that he hadn't expected them to be human once. During this, a strange light approaches and Gengar backs off, no longer causing pain through Dream Eater but still looking into the dream. From this, Gengar sees Gardevoir speaking to the player and learns that the player was brought to the Pokémon world to save it from destruction by a falling star. Gengar also hears that Gardevoir hasn't forgotten about her partner from long ago, nor does she hate him, even though he was the cause of her current state, an agent of spirits with no physical form. Heartbroken by this, Gengar stops looking into the player's dream and runs off, crying.
Following this revelation, Gengar decides to assist the player and partner from behind the scenes. He first does this by helping Alakazam and Xatu create the Teleport Gem needed to reach Sky Tower, hiding afterwards. After Rayquaza is defeated and convinced to destroy the falling star, the resulting explosion seemingly kills the player and partner, casting their spirits adrift. Gengar saves them by leading their spirits back, under the pretense of attempting to drag them to "the dark world", losing his way, and "ditching them" in an attempt to preserve his antagonistic image.
In the post-game, Medicham appears just to the east of the rescue team base, telling the player about a "funny" story she heard about Lombre apparently drowning out at sea. This allows the player to hear the real story from Lombre himself, ultimately leading them to the Stormy Sea.
After clearing Pitfall Valley and gaining access to the Sky Blue Plains, Medicham and Ekans appear at Whiscash Pond for two days. On both days, they talk amongst themselves about a dungeon they had discovered and kept secret from even Gengar, a wondrous cave where wishes are said to come true; once they notice the player, they panic, deny knowing anything about such a place, and leave. On the third day, Ekans appears at the pond on his own, having explored their secret dungeon only to be knocked out, with Medicham still trapped inside as evidenced by her rescue notice later arriving on the bulletin board. This notice grants the player access to this secret dungeon, Wish Cave, with the player receiving the Wish Stone from Medicham as a reward.
After clearing Stormy Sea and rescuing Medicham, she and Ekans appear at Pelipper Post Office, again talking amongst themselves; this time, they mention that Gengar won't do anything wicked with them anymore and has generally been acting strange lately, as if he has a lot on his mind. The next day the duo is seen at the central area of Pokémon Square, where they mention that Gengar has begun climbing Mt. Freeze, presumably to reach Ninetales. The following day, Gengar approaches the player as they leave their base, asking them to help him reach the peak of Mt. Freeze, as he can't make it on his own.
At the peak, Gengar speaks to Ninetales, revealing that he was actually the human from the legend; Ninetales states that the human became Gengar because he ran from both himself and Gardevoir back then. Gengar tells Ninetales to lift the curse on Gardevoir, even threatening to make the player defeat it if he has to. Ninetales retorts that even defeating it wouldn't lift the curse, but it mentions that there may be another way. It goes on to say that it was enraged at Gengar's "twisted" heart, which was the target of its curse in the first place; depending on Gengar's heart now, the curse may be lifted. It gives Gengar the 9-Tail Crest and directs him to Murky Cave, where he might be able to unseal Gardevoir's physical form. As Gengar and the player leave, Ninetales notes that Gengar has changed, citing his old and new emotions clashing within his heart.
As early as the next day, the player escorts Gengar to the depths of Murky Cave, where he places the 9-Tail Crest into a dais. Following this, they are greeted by a mysterious, apparently formless being known only as the "judge of darkness", who asks if they have come to break the curse on Gardevoir. Gengar affirms this, but the "judge" states that it has to evaluate Gengar first. Gengar asks if this means facing a boss creature, and the "judge" replies that it only needs some questions to be answered, though it immediately immobilizes Gengar and asks the player to answer in his stead, stating that Gengar will likely never reveal his true feelings.
The "judge" sends the player into Gengar's heart to answer its questions, and once that is done, it renders its judgment, stating it could not lift Gardevoir's curse. Desperate, Gengar breaks the seal immobilizing him and begs for a chance to say his piece. He admits that he abandoned Gardevoir to save himself, and he was quick to forget about her and the curse, living his life as a human and as a Gengar without a care. However, in the player's dream, he learned that Gardevoir never forgot about him, and even considered him to be an irreplacable friend despite what he had done to her, showing him how selfish he had been; he even mentions how the player's team had put up with his selfishness and brought him to this point. This makes him realize what he had been lacking all this time: a sense of gratitude.
This realization breaks the curse and releases Gardevoir's physical form. Ninetales appears and congratulates Gengar, stating that his newfound sense of gratitude was the true key to breaking the curse. It also mentions that Gardevoir will awaken soon, but with no memory of ever being Gengar's partner; Gengar is simply grateful that she is no longer cursed, stating that this is enough for him. Later, at the rescue team base, Gardevoir expresses her gratitude to the player and Gengar for saving her despite "never meeting before". Gengar also thanks the player by giving them a Mobile Scarf. As he leaves, Gardevoir asks for his name, and Gengar "introduces" himself to her.
Neither Gengar, nor Medicham and Ekans, appear again in the game after this point. It isn't known what happened to them.
Mt. Freeze and Murky Cave
*Aside from Taunt, Gengar can't learn any of these moves legitimately.