After returning from the fierce battle on Treasure Island, Senku and the Kingdom of Science use the petrification device they obtained to successfully revive Tsukasa Shishio, who joins their cause. With their coalition stronger than ever, Senku determines that the mastermind behind humanity’s petrification, an entity they call Why-man, is located on the moon. To uncover the final truth, Senku launches an ambitious project to build a spaceship from scratch in the Stone World.

The Kingdom of Science immediately sets sail on the Perseus to gather the necessary materials from across the globe. Their first destination is the American continent, where they seek a massive quantity of corn, the raw material needed to mass-produce the revival fluid. However, upon arriving in what is now California, they discover they are not alone. Dr. Xeno, a brilliant former NASA scientist and Senku’s childhood science mentor, has built his own militarized scientific empire. Alongside his elite sniper and right-hand man, Stanley Snyder, Xeno commands advanced technology and believes in using science to establish order through force, putting him on a direct collision course with Senku’s philosophy of science for liberation.

What follows is a war of ideologies as Senku and his friends find themselves targeted for assassination by Xeno’s forces. The crew of the Perseus must engage in tactical maneuvers, espionage, and aerial dogfights to survive against this new scientific superpower. After a series of strategic battles, Chrome leads a successful mission to capture Dr. Xeno. Fleeing Stanley’s relentless pursuit, Senku’s group takes Xeno hostage and charts a course for their next destination: South America.

The team heads to the Amazon rainforest, the epicenter from which the original petrification beam originated. Here, they delve into the secrets of the Medusa devices, the mysterious mechanisms responsible for the global catastrophe. In a shocking turn of events, a second worldwide petrification event is triggered, turning all of humanity to stone once again. Years pass in this desolate world until Suika, who was revived alone due to her small size, manages to survive for seven years in solitude. Using Senku’s old roadmap and tireless trial and error, she successfully recreates the revival fluid and awakens Senku, restarting the mission to save humanity.

With the revived Dr. Xeno now cooperating as a valuable ally and the key to controlling the Medusa devices within reach, the Kingdom of Science emerges from the second petrification with a renewed goal. The final stage of their plan commences as they begin the monumental task of building a spacecraft to launch for the moon, where the mysterious Why-man awaits, holding the final answers to the fate of the human race.