For many years, the plague's origin was thought to be Elysia, but in YE 29, it was revealed that the plague was a biological weapon created by PNUgen Corporation. It is speculated that the real motive behind the plague was elimination of humans who refused to change to PNUgen-produced Geshrin bodies via Soul Transfer technology, giving the corporation a monopoly on a whole species and thus able to control the Yamatai Star Empire.
In response to the revelations, the Star Army of Yamatai attacked and destroyed PNUgen facilities and the government dissolved the corporation permanently.
The Great Plague was a sophisticated biological weapon that activated telepathic capabilities in humans. Once a victim was infected, looking at another person caused the virus to select that person as a target for the infection to spread to via telepathic attack. When the people made eye contact, the infection silently spread.
The infected showed no symptoms and they were all on a synchronized timer so that five years after the virus was initially released in YE 03, once almost everyone on Planet Yamatai was infected, it killed them all at once. This also means there are no carriers left and the plague wiped itself out.