The game takes place in the far future, where mankind has recently developed technology allowing them to quickly travel to other planets. One day, Earth receives a telepathic distress call from Princess Irene La Tias (also known as Elaine La Tias), whose home planet E-Square has been taken over by Lord Klaus Pachelbel and his bio-mechanical army. Humans soon also discover the mysterious alien life form "Flint", and quickly assemble a new space fighter, the Flintlock TMF01, that is capable of carrying the Flint with it. The Flintlock and Flint are then sent out to save Irene and her planet.