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The story is set in the Gurhal Star System (A system comprised of three planets, like Algol from the original Phantasy Star games), and follows the events of Ethan Waber and the Guardians after an alien force known only as 'THE SEED' invades all three planets.
100 years before this, the three planets, Moatoob, Parum and Neudaiz signed a treaty ending the greatest of their inter-planetary wars, known as The Final Conflict. This led to the birth of the Allied Army. Celebrating the 100th anniversary of this, the Allied Army went on a flight. This was naturally a huge event, with millions of people from around the system watching, and everything was going fine until what seemed to be meteorites collided with the fleet, completely destroying it. The entire fleet was lost, and onlookers could do nothing as THE SEED assaulted the planets and the space station known as the GUARDIANS Colony. THE SEED then began its hostile takeover of the Gurhal System. The linear line was under attack, and Ethan and his sister were separated. The game starts off as Ethan trying to find a way to find his sister. After this event, he becomes a guardian, and goes on various missions, a deep plot unfolding, surrounding THE SEED, Mirei, and Karen...
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