All About Lily Chou-Chou follows two childhood friends, Shusuke Hoshino and Yuichi Hasumi, from the end of their junior high school run until the beginning of high school. The film has a discontinuous storyline, starting midway through the story, just after high school begins, then flashes back to junior high and summer vacation, and then skips back to the present. In junior high, Hoshino was the best student in school, but was picked on by his classmates. He was skilled at kendo, and had a good-looking young mom. Yuichi, on the other hand, was a quieter boy who fell in love with the music of the odd musician Lily Chou-Chou. During a group trip to Okinawa, Hoshino had a traumatic near-death experience and his personality changed from good-natured to dangerous and manipulative. In high school, he takes his place as class bully and shows his newfound power by ruining the lives of his classmates. An alternative voice, that of the character Sumika Kanzaki, attributes Hoshino's personality change to divorce and family ruin; this matches several scenes connecting the decline of Yuichi - who has had to change his name - to divorce. Yuichi, the confused and shy former friend of Hoshino, finds himself sucked into his now-tormentor's gang. He is ridiculed and coerced into doing Hoshino's dirty work, and finds solace only in the ethereal music Lily Chou-Chou makes. Things become far worse for everyone when Yuichi is assigned to supervising Shiori Tsuda, whom Hoshino has blackmailed into enjo ksai, and another girl is raped by Hoshino's lackeys after unwittingly offending the school's girl gang. The whole quagmire comes to a head when Yuichi heads to Tokyo to see a Lily Chou-Chou concert, and encounters the last person he thought would be there. The story of Hoshino and Yuichi is paralleled by messages posted to a Lily Chou-Chou Internet message board which are displayed on screen. It is left up to the viewer to figure out which characters in the story are posting under what names.