On September 9, 2005 at 9:09:09 PM, nine pro baseball players witnessed a glowing ball in the night sky. Among them, Atsuya Furuta met a man named J. Shuro who told him about the legendary Astro Ball Team created from the dreams of baseball great Eiji Sawamura, sparking Furuta's deep intrigue.

Shuro begins the search for the Astro Nine with Kyuichi, starting with Kyugo, a baseball prodigy raised by Nagashima from an orphanage. Although Kyugo bears the mark of a superhuman he refuses to join the Astro team out of loyalty while Shuro later shows Kyuichi footage of twin superhumans, Kyushichi and Kyuhachi, who have incredible defensive abilities.

Kyuichi and his team confirm Kyusaburo Ijuin as a true Astro superhuman, then discover another marked boy, Kyuni, with extraordinary skills. Despite these successes their search for the remaining superhumans faces challenges, culminating in an incident at a high school in Aso.

Just before Kyuichi's showdown with Ryu, Shuro appears in a helicopter, dropping the body of Kyusaburo who had died in a race accident. The shock revives Kyusaburo, halting the duel as the team celebrates while Lotte’s manager Kaneda prepares to confront the Astro team.

In March of 1973 the special match between the Astro Ball Team and Lotte takes place on Ganryu Island but Shuro leaves the team, urging them to win on their own. Kyuichi and the team, understanding their destiny, vow victory with Kyuichi's pitching overpowering even Ryu despite Lotte's manager Kaneda's taunts.

Kyuichi's pitch is hit by Joe and Kyushichi injures his hand trying to catch the ball, leading Kyuichi to lash out at his teammates in frustration. Meanwhile Kyuni struggles with Lotte's pitches but Kyuta offers him encouragement as a mysterious man in a school uniform mocks a group watching the game.

The Astro Nine team, divided due to frustrations and injuries, discovers that Kyushichi has been secretly playing while injured, leading to a renewed sense of unity. Kyuhachi avenges his brother by striking out Joe while Kyuichi, after a motivational dream with Eiji Sawamura, decides to create a new magic pitch as Ryu prepares to take the mound.

Kyusaburo realizes Ryu's L-shaped pitch is deadly but Kyuni ignores the warning and tragically dies. As the team mourns, Kyuta gains superhuman powers after being struck by lightning, reviving the team's spirits. The game resumes with a battered Kyusaburo stepping up to bat, prepared to confront Ryu's lethal pitch.

Shuro and the Astro Nine mourn Kyuni but struggle to accept Ryu, their former enemy, as a teammate. While Ryu is grieving alone a mysterious man provokes him and Shuro heads to Korakuen Stadium to arrange the next game where he encounters Chairman Toge.

The Astro Nine grows worried when they learn Kyushiro is the grandson of the pro baseball association's first president while he recruits athletes like boxing champion Dynamite Ken and former sumo wrestler Rikudouiwa for his new Victory Team. At his press conference the Astro Nine confronts armed martial artists blocking their way.

Shuro convinces Kyushiro to agree to a match between Astro and Victory with the condition that Kyushiro will join Astro if he loses. Meanwhile at the Jinnryu Kenpo dojo in Kagoshima, Kyusaburo encounters the Ijuin brothers, revealing their complicated history, before confronting Ryu who is considering joining Victory but Ryu rejects Kyusaburo's plea to stay with Astro.

Kyusaburo learns that Daimon killed his father to settle a family feud, planning to eliminate him as well, despite their childhood bond. As he prepares for the Victory match, Kyusaburo reaffirms his commitment to the Astro Nine while Kyuichi endures grueling training to develop a new magic pitch.

The Astro vs. Victory match begins with Kyuichi's sharp pitches stunning Dynamite Ken and Astro making a strong start. However, Kyushiro seems to have a hidden strategy while Daimon counters a hit with a deadly kick and the mysterious pitcher Ujiie invokes fear as the Victory team chants "Namu Amida Butsu," prompting Nagashima to recognize Ujiie as a legendary beanball pitcher.

The Astro team endures serious injuries from Ujiie's deadly pitches with Kyuichi hitting a home run before Ujiie transforms into an elderly man. Kyushiro vows to eliminate Astro and a trap results in Kyugo being gravely injured, intensifying the team's anger.

Baron Mori joins the Victory team, baffling both sides with his flamboyant demeanor and inexperience. While Kyuushiro remains calm, Baron shifts from timid to aggressive, confronting his teammates. The game progresses to Daimon who taunts Kyuichi with nunchaku but Kyuushiro intervenes, forcing Kyuichi to walk Daimon which only fuels Daimon's anger.

Daimon attacks Kyuushiro but collapses after hitting a home run, having been mortally wounded. As Kyuushiro reads an apology, Kyuichi's anger ignites a counterattack from Astro while Baron encourages Kyuushiro to embrace the true spirit of baseball.

Kyuushiro's right arm is incapacitated, yet the superhumans' spirits soar. Baron chases a foul ball, injures his head and hits a powerful home run but collapses before home plate, bleeding from his nose and mouth.

The match concludes with Kyuugo walking on a full count, securing victory for the Astro team. Defeated, Kyuushiro attempts seppuku but is stopped by Hino Kyuukuro. Soon after a newspaper reports the Astro team's disapproval by professional baseball.