Ico, a horned boy, is taken by a group of warriors to an abandoned castle and locked inside a stone coffin to be sacrificed. A tremor topples the coffin and Ico escapes. As he searches the castle, he comes across Yorda (ヨルダ Yoruda?), a captive girl who speaks a different language. Ico helps Yorda escape and defends her from shadow-like creatures. The pair make their way through the castle and arrive at the bridge leading to land. As they cross, the Queen, ruler of the castle, appears and tells Yorda that as her daughter she cannot leave the castle. The Queen destroys part of the bridge; although Yorda tries to save him, Ico falls off the bridge and loses consciousness.

Ico awakens below the castle and makes his way back to the upper levels, finding a magic sword that dispels the shadow creatures. After discovering that Yorda has been turned to stone by the Queen. He confronts the Queen in her throne room, who reveals that she plans to restart her life anew by taking possession of Yorda's body. Ico slays the Queen with the magic sword, but with her death the castle begins to collapse around him; he is hit by falling debris, breaking his horns, and he falls unconscious. The Queen's spell on Yorda is broken, and a shadowy Yorda carries Ico safely out of the castle to a boat, sending him to drift to the shore alone. Ico awakens to find the distant castle in ruins, and Yorda, in her human form, washed up nearby. She stirs.