Natsuza Yuzuki has been playing rugby as a left-winger ever since he was a child. After enrolling in Doushisha University, he quickly becomes a rising star in the Kansai University League. His dreams are shattered, however, when a nasty motorbike accident leaves him with a spinal hernia—making him unable to be able to play rugby ever again. With no role available other than the position of manager, he accepts his new post and hopes his squad can obtain a league title. Yuzuki's team is an unlikely group, including his stoic best friend and full-back Seiichirou Jingyouji; hot-headed first-year Yasunari Tsuru, who harbors a strong dislike for Natsuza, filling his senior's old position as left wing; and Yuu Mashiro, who is struggling to hold his ground as a scrum half. Despite Natsuza putting his all into training his team for a league title, their squad still feels incomplete. A year ago, Ibuki Ueka, the genius fly-half that was once Doushisha's ace, suddenly quit rugby—and now Natsuza is determined to get him back.

Thanks to the sacrifices of war heroes like Amuro Ray, the Universal Century's 105th year sees an era of hard-won but short-lived peace. The Earth Federation keeps a militaristic hold on the planet and its surrounding space colonies. Although Char Aznable's rebellion against the neglectful Federation met its ultimate failure, his revolutionary philosophy of true freedom for all human beings lives on. Despite being the son of a famous Federation commander, Hathaway Noa embodies both the undying loyalty of soldier Amuro Ray and the militant passion of rebel leader Char Aznable. Haunted by memories of Char's Rebellion, Hathaway leads a dissident faction of his own known as Mafty. He adopts the alias Mafty Navue Erin and commits acts of violence in revolt against the growing tyranny of the Federation. After thwarting the hostile takeover of a plane by a terrorist group fraudulently claiming to be Mafty, Hathaway's secret identity is discovered by a young woman named Gigi Andalucia. Hathaway befriends both Gigi and Federation colonel Kenneth Sleg, but his double life endangers them as the armed conflict between Mafty and the Federation comes to a head.

In August of 1995, Mikiya Kokutou meets a young kimono-clad woman named Shiki Ryougi. When he finds out that they go to the same school, he attempts to befriend her. Though her upbringing is unconventional and she herself is strange, Mikiya is not deterred, and Shiki gradually opens up to him. But Mikiya's life will be changed forever by this simple meeting, and in ways that he never imagined, as he begins to see a deadly side to his new friend...

For blasé college dropout Tsunehiro Sasaki, life has become hopeless. After failing to enter a top university, he has lost all his money trading on financial markets and is now critically indebted. To add to his misery, he learns that he only has at most two years left to live due to an incurable disease. The trajectory of Tsunehiro's life suddenly changes after a group of amateur fishermen saves him from drowning as he was trying to escape from a trio of creditors. While Takaaki Tsutsujimori pushes Tsunehiro to work at the group's workplace—a convenience store that doubles as a fishing shop—Hana Ayukawa tries to share her love for fishing. Although the attempts of the joyful group of anglers initially prove unsuccessful, Takaaki urges Tsunehiro to take a fresh start in life, and the young man eventually accepts the fishing enthusiast's assistance to pay off his debts. As work, friendships, and an unfamiliar hobby all suddenly find their way into his life, Tsunehiro must find the strength to change his ways if he wants to make the best of his remaining time.