After five years of harboring unspoken feelings, high-schooler 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.

Souma Yukihira has been cooking alongside his father Jouichirou for as long as he can remember. As a sous chef at his father's restaurant, he has spent years developing his culinary expertise and inventing new dishes to amaze their customers. He aspires to exceed his father's skill and take over the restaurant one day, but he is shocked to learn that Jouichirou is closing up the shop to take a job in New York. Rather than tagging along with his father, Souma finds himself enrolling at the prestigious Tootsuki Culinary Academy, where only 10 percent of its students end up graduating. The school is famous for its Shokugeki—intense cooking competitions between students often used to settle debates and arguments. Jouichirou tells Souma that to surpass him and survive the next three years at Tootsuki and graduate there. The academy's brutal curriculum and fiercely competitive student body await the young chef, who must learn to navigate the treacherous environment if he wants to stand a chance at realizing his dreams. But is skill alone enough to let him rise to the top?

The qualifiers of the Autumn Elections are now over, and only eight talented chefs remain. Now, they face off in one-on-one food wars, each with their own unique themes. Met with both new judges and new opponents all with their own specialties, Souma must stay on his toes if he hopes to make it to the top of both the Autumn Elections and Tootsuki Culinary Academy.

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 the snow melts and 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!