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They all died, thats it, whats confusing? Or are you wanting a detailed story of their death?
Before the grandma died, his parents are just living in the city right?
His parents are also living with him. See that page where Midori revived him and he was welcomed by his mother and grandmother. Probably his father was working that time. Most likely his parents left for a trip and they had an accident on the way. While his grandmother had a sickness and died.
I'm confused about the family background story though.. (￣∇￣")