January 1st, 2009. A truck crashes in the middle of Shibuya, Tokyo. Kairi Nakajo wakes up in a hospital with total amnesia. Soon after, his parents break to him the news that they have decided to move to the tranquil city of Kujikawa. Kairi is forced to go with them, basically cutting off every direct link to his past.
Three years have passed, but therapy has failed and Kairi has not managed to get any of his memories back. In the meantime, he has grown suspicious of his parents, who appear to have been trying to replace his missing memories with new ones. The new memories seem to have been carefully chosen in order to mold a new Kairi, who would more closely resemble their ideal son.
Tokyo has changed as well: thick clouds are covering its sky and a dreadful case of serial abductions threatens its residents. And it appears that it all started on the day of Kairi's fateful accident...