SEGA re-released in 2003 an updated version of Phantasy Star Online Episode I & II for the Nintendo GameCube in 2003 called Phantasy Star Online Episode I & II Plus.

Early in the effort to run unsigned code on the GameCube, people found that when playing PSO and connecting to a server using the GameCube Broadband Adapter, a regular PC could be made to pretend it was a server which would fool the game.

After making the connection, data could be streamed back to the GameCube, making it easy for hacking and false servers. Phantasy Star Online Episode I & II Plus was created in mind to fix this problem. Along with this problem, SEGA included extra content for offline with this game including:

- Episode II Challenge Mode, which was perviously only online.

- Perviously Online only quests, Seat of the Heart, West Tower and East Tower are now available offline.

- Central Dome Fire Swirl, a downloadable quest for the Xbox, is now available offline.

- The downloadable goods from Fake in Yellow quest are now available offline.

Aside from some extra cheat protection, Phantasy Star Online Episode I & II Plus ran exactly the same as the original version and all data from characters, items, ect, can be swapped between the two instantly.