In the games
Shiftry is the leader of Team Shifty. He is first seen when a Jumpluff asks him to save its friend, another Jumpluff, at Silent Chasm who had gotten stuck as Shiftry could use his fans to free it. Shiftry refuses at first, but Alakazam tells him to go and rescue Jumpluff, so he does. However, he never returns. The player and partner then go and rescue Jumpluff but Zapdos takes Shiftry hostage to Mt. Thunder. The player and partner then head up Mt. Thunder and defeat Zapdos, who then lets Shiftry go.
When the rescue teams are pursuing the player and partner, Shiftry pulls out at Mt. Blaze because the fire would burn him. When the player and partner return, he was happy to find out that they were not responsible for the natural disasters. Shiftry then assembled a team to go and defeat Groudon.
Shiftry was present at Hill of the Ancients and was sad to see the player leave as he had never said thanks for the player saving him.
Shiftry later returns in Super Mystery Dungeon, where he is one of the fainted Pokémon across the different dungeons and will be recruited once the player finds and feeds him. Upon connecting with him, he will comment that he was previously kidnapped by Zapdos, but he was able to escape. While on the run, he eventually collapsed due to hunger.
For more information on this Pokémon's species, see Shiftry.