After five years of harboring unspoken feelings, Taiju Ooki is finally ready to confess his love to Yuzuriha Ogawa. Just when Taiju begins his confession however, a blinding green light strikes the Earth and petrifies mankind around the world—turning every single human into stone. Several millennia later, Taiju awakens to find the modern world completely nonexistent, as nature has flourished in the years humanity stood still. Among a stone world of statues, Taiju encounters one other living human: his science-loving friend Senkuu, who has been active for a few months. Taiju learns that Senkuu has developed a grand scheme—to launch the complete revival of civilization with science. Taiju's brawn and Senkuu's brains combine to forge a formidable partnership, and they soon uncover a method to revive those petrified. However, Senkuu's master plan is threatened when his ideologies are challenged by those who awaken. All the while, the reason for mankind's petrification remains unknown.

Senkuu has made it his goal to bring back two million years of human achievement and revive the entirety of those turned to statues. However, one man stands in his way: Tsukasa Shishiou, who believes that only the fittest of those petrified should be revived. As spring approaches, Senkuu and his allies in Ishigami Village finish the preparations for their attack on the Tsukasa Empire. With a reinvented cell phone model now at their disposal, the Kingdom of Science is ready to launch its newest scheme to recruit the sizable numbers of Tsukasa's army to their side. However, it is a race against time; for every day the Kingdom of Science spends perfecting their inventions, the empire rapidly grows in number. Reuniting with old friends and gaining new allies, Senkuu and the Kingdom of Science must stop Tsukasa's forces in order to fulfill their goal of restoring humanity and all its creations. With the two sides each in pursuit of their ideal world, the Stone Wars have now begun!

With the ambitious Ryuusui Nanami on board, Senkuu Ishigami and his team are almost ready to sail the seas and reach the other side of the world—where the bizarre green light that petrified humanity originated. Thanks to the revival of a skillful chef, enough food is being prepared for the entire crew, and the incredible reinvention of the GPS promises to ensure safety on the open sea. Preparations for the upcoming journey progress swimmingly until Senkuu receives an eerie message from a mysterious source. More driven than ever, the scientist sets out to explore the new world and discover what it can offer for his scientific cause. Though the uncharted territories may hide unkind surprises, Senkuu, with a little help from science, is ready to take on any challenge.

Having resolved the crisis in the Petrification Kingdom, Senkuu and his companions gear up to deal directly with the mastermind behind the petrification phenomenon—who supposedly resides on the moon. The ambitious spaceship project, however, requires immense manpower and critical resources scattered across the world. Thus, the Kingdom of Science exploration team kick-starts its transcontinental journey on the ship Perseus to gather them all. Equipped with modern technology and bolstered by the new, capable members in their ranks, the exploration team feels confident about setting sail to their first destination: America. They soon realize that the region now hosts adversaries controlling the resources they need, doing so with scientific technology which rivals and even exceeds their own. In a battle of science versus science, Senkuu and his team must outsmart their rivals if they are to have any chance of ensuring the continued survival and rejuvenation of humanity.