EB64's story was divided into chapters, but unlike the 8 chapters the Mother 3 on the GBA would receive, the original game was intended to have 12. In the May 2000 issue of the magazine "64 Dream", Itoi states in an interview: "I really might need to cut back on Chapter 12."
Throughout these, players would play as different characters, much like the GBA title. These chapters were not independent of one another; sometimes you might run across characters from other chapters or see some events from different people's perspectives.
The first chapter was to take place in Tatsumairi (sometimes spelled Tatsumari, the official spelling is unknown, but this was what was essentially Tazmily in Mother 3. This chapter, you would take control of Flint.
In addition, the chapters would span over the course of 10 years, where characters would visibly grow and mature. While the final game continued with a similar idea, there was a time skip of only three years, so what differences there would have been remain unknown.