The Story of Defender GBA is mainly focused on the arrival of the second Manti Swarm, as well as the inavsion of Earth. And the founding of Cydonia Base Mars. The player flies as an unidentified member of the GSA, attemting to help the GSA evacuate mankind from Earth and move them to other parts of them galaxy. The player's ultimate goal is to keep mankind safe as they prepare to attack the next swarm.