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In the beginning of his story mode, Gamma is awoken by Dr. Eggman and is soon pitted against his "older brother" Beta to see which of the two would be worthy of working on Eggman's carrier. Beta is defeated, and Gamma is officially recruited onto Eggman's ship.
Gamma's first official mission is to find a frog that has Chaos' tail and a Chaos Emerald. After this, his next mission is to get a bird from a girl that is locked up inside the ship. As Gamma makes his way to the room, he accidentally walks into the opposite room and discovers the fate of Beta after finding another robot being created and seeing parts from Beta's body lying nearby. This image stays with Gamma throughout the rest of the story as a conscience slowly builds inside of him.
As he continues with his mission, he finds Amy Rose is the one who is locked up on the ship. She begs Gamma to let her and the bird go, and eventually agrees to do so. After a brief fight with Sonic and another short chat with Amy, Gamma decides to leave Eggman and "rescue" his other E-100 siblings by destroying them and releasing the animals inside of them.
At the end of Gamma's story mode, he has a final showdown with an upgraded Beta and is again victorious, but suffers a fatal shot from Beta before it explodes. Gamma notices the bird that is freed from Beta and an image of three birds appears (the one Amy had, the bird freed from Beta, and an unknown bird) As the freed bird flies away, Gamma eventually explodes due to Beta's shot. In the last shot from his story, the third bird is revealed to be the one trapped in Gamma's body.