Tails starts out by experimenting with putting an emerald in his plane, but he crashes down and Sonic saves him. Together they go to Mystic Ruin where Eggman attacks in his Egg Hornet. He takes Tails' emerald, so together Sonic and Tails go on a quest to collect all the emeralds before Eggman can. They head for Windy Valley, Casinopolis, and Ice Cap, collecting three emeralds before battling with Knuckles in Mystic Ruins. Eggman takes the emeralds and gives them to Chaos, so the trio battle Chaos 4.
Tails takes Sonic in his plane to chase Eggman's Egg Carrier, bit they get shot down. Tails lands in the jungles of Mystic Ruins where he has a sad dream of running alongside Sonic but not being able to catch up with him. He comes to and sees Froggy, and chases him though Sand Hill. After he catches him, he takes the emerald from Froggy and Big runs by and sends Froggy hopping off again. Tikal light whisks Tails away to the Echidna Village and speaks to him.
Tails heads back to his workshop and repairs his plane, then goes to Red Mountain to get Sonic and go after the Egg Carrier again in Sky Chase 2. They head through Sky Deck and find Amy. Sonic tells Tails to take Amy back to Station Square, so he picks her up and flies her down. When he gets there, he sees Eggman has launched a giant missile into Station Square but it hasn't detonated. He decides to be brave and chases Eggman through Speed Highway to get to the missile before him and keep it from detonating. Tails heads to the Casino area, where Eggman attacks in the Egg Walker. Tails cleverly defeats him, and the people of Station Square cheer for their young new hero.