Some background: ZUN released the full version of Touhou 9 at Comiket 68 on August 14, 2005.
The premise of the story is that the protagonists are investigating an abnormally high number of blooming flowers. At the end of the story, they find out that the flowers are blooming because of a sudden spike in the number of deaths. It's also revealed that a similar flower incident occurred 60 years ago. This lines up with events from the end of World War II in 1945 (including the Battle of Okinawa and the atomic bombings of Hiroshima and Nagasaki).
But this implies that there was another event with a large death toll in 2005. So my question is: Was there a specific event in real life in 2005 that ZUN might have been referencing?