Whenever a character used a Duel Capsule or initiate a duel on the board, a Fly Guy would come down to carry them off to the mini-game.
Fly Guys also appear in a handful of mini-games as well. In Mecha-Marathon, the characters must twist a wind-up key in order to initiate their mechanical Fly Guy in the race.
Mario & Luigi series
Fly Guys appear in Mario & Luigi: Partners in Time, where they carry timed bombs in battle. They may also carry Goombas and dropped them on Mario/Luigi's head.
Fly Guys reappear in Mario & Luigi: Dream Team, behaving similarily to the previous game. This time though, they are able to summon Goombas.
Only a few Fly Guys appear as enemies in Mario & Luigi: Paper Jam during specific Paper Toad missions. They do not use Goombas for any of their attacks. Instead, they mostly rely on a bomb they toss back and forth to one another to attack.
Fly Guys appear in the remakes of Mario & Luigi: Superstar Saga and Mario & Luigi: Bowser's Inside Story. In both games, they only appear in the Minion Quest modes, acting as strong flying soldiers against Ice Bros and Biddybuds.
Paper Mario Series
Fly Guys are set to make their debut in the series as Folded Soldiers in Paper Mario: The Origami King.
In the Super Smash Bros. series, the Fly Guy appears in the stage Yoshi's Island seen carrying food, if you hit the Fly Guys, they will drop the food and fly away.
Fly Guys exist unused in New Super Mario Bros. Wii, being removed from the final game.Fly Guys were also set to appear in Super Paper Mario before being scrapped.