Makunouchi Ippo is the new Featherweight champion of Japan and is now ready for his first title defense. His opponent, the former Jr. Featherweight champion and a medical student, Sanada Kazuki. In addition to this feud, Sanada is being coached by Kamogawa's former rival, Hama Dankichi. What makes things worse is that Sanada works at the same hospital where Kumi is a nurse at and everybody at the hospital wants Sanada to win. Not only does Ippo have to defend his title, he has to reclaim his love.
Set during the Inter High Championships, Shohoku take on Tsukubu, one of this year's dark horses. It's a clash of acquaintances as Anzai will face his former student which is now the coach of Tsukubu, while Akagi & Kogure meet Godai their former classmate and Tsukubu's captain. Finally Sakuragi is irked by the presence of Nango, Tsukubu's center, who vies for Haruko's attention.
The third Captain Tsubasa movie is basically about a training match of the All Japan Boy Soccer Team, but most of the time you see flashbacks of former matches, for instance the final match Nankatsu vs. Toho or when Wakabayashi challenges team captains of different sports.