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.

In Penguin Village, humans live alongside talking animals and objects. Senbei Norimaki is one of these humans, and he's an inventor with the lofty dream of creating the world's best robot girl. The product of his efforts is Arale, but depending on your definition of perfect, she's anything but! Not only is Arale severely nearsighted, but she also has no common sense! At least she has super-strength, though that often proves to be a setback as well. Although she means well, Arale only causes trouble for her neighbors in the whimsical Penguin Village!

Now that brains and brawns have united forces, the next step in Senkuu's plan to unravel the mystery behind the green light that once petrified humanity is to go to the other side of the Earth and investigate its origin. However, to achieve this, Senkuu must first build a ship. With the help of Tsukasa Shishiou's former underlings, the base of the ship is rapidly assembled, but there is one missing piece: a skilled captain. During their search, Senkuu and his crew come across a petrified Ryuusui Nanami—the heir of the biggest maritime conglomerate, known for his vast knowledge of sailboats but unpleasant personality. Despite this, Senkuu takes the risk and revives Ryuusui. Ryuusui, upon realizing there are no ownership rights in this new civilization, is excited at the prospect of claiming everything for himself. But before he agrees to play a crucial part in their upcoming journey and command the vessel through the restless seas, he and Senkuu must find the king of fuels to power the ship—oil.

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!