The Phantasy Star Online series takes place on a fictional planet, Ragol and the desperate attempt by the people aboard the spaceship Pioneer II to colonize the planet. There are four different episodes in the story line, spanning a time of 21 years. (Note: Although it is titled Episode IV, it occurs chronologically prior to Episode III. Upon its creation, SEGA claimed that Episode III would be the final episode in Phantasy Star Online's story arcs. However, with the release of Blue Burst a year later, Episode IV was added)
Episode I: Seven years after Pioneer I landed on Ragol to colonize the planet, Pioneer II finally arrives in orbit around the planet. While preparing to land, a large explosion rocks the surface of Ragol and cuts off any communication between Pioneer II and the colonists down below. The Principal of Pioneer II issues the order that Pioneer II shall remain in orbit until what happened on the surface could be understood. In an attempt to discover the cause of the explosion, the Principal enlists the help of Hunters to explore the surface of Ragol for clues about the mysterious explosion and the whereabouts of his daughter, Rico Tyrell.
Episode II: Takes place shortly after Episode I. The discovery of a formerly unknown laboratory on Gal Da Val island peeks interest in Pioneer II's government and once again recruits the hunters for help. While searching the newly discovered area, mysterious voice fragments of Healthcliff Flowen, a military commander presumed dead by the government, are uncovered. Using these messages as a map, the hunters now both explore the mysterious new laboratory, as well as discover the fate of Healthcliff Flowen and the terrible plan of Dr. Osto.
Episode IV: Takes place about 2 years after Episode II. Still searching for a place to land to begin colonization, a comet en-route for Pioneer II is deflected by the ship, causing it to smash into the surface of Ragol with terrible force. From the mysterious crash, large amounts of photon were detected, causing Pioneer II to take interest. The Principal once again calls upon the hunters to travel into the crater to research the effects of the recent asteroid collision.
Episode III: Takes places 21 years after the events of Episode II. Pioneer II's government, which is now independent from Coral, is filled with inner strife over to exploit the resources on Ragol, which would keep them from colonizing the planet. Among them is a a mysterious “germ” which was used to create the new C.A.R.D. technology. The Hunters, a government run organization that was created with the purpose in mind to research and find the source of the “germ”, is now within conflict with the terrorist organization Arkz, who oppose any means to exploit the mysterious new substance.