At the dawn of the modern era, Portuguese explorer Ferdinand Magellan leads an expedition under the Spanish crown in search of the first westward route to the Spice Islands. He embarks on a perilous journey across the uncharted Pacific, where his fleet faces starvation, mutiny, and the psychological toll of endless seas. Upon reaching the shores of Cebu, Magellan is pulled into a fatal conflict with the natives by his drive to spread Catholicism, culminating in his tragic doom.

Hilarion Zabala has a mysterious, recurring olfactory problem. A counselor/psychiatrist suspects a lingering case of phantosmia, a phantom smell, and possibly caused by a deep psychological fracture. One recommended radical cure is that Hilarion must go back and deal with the darkest currents of his past life in the military service. Reassigned in the very remote Pulo Penal Colony, he must also confront the horrific realities of his present situation.

Tomas, the old venerable mayor of the remote town of Kawalan, learns that the invading Japanese will set up a garrison there. He organizes willing members in his community to set up a hidden settlement in the middle of the forest, where they can live unaffected by the horrors of war. As a young revolutionary during the 1896 fight against Spain and then as a soldier fighting against the Americans, Tomas had witnessed the effects of violence on people and become a pacifist. Now, he must see if inhabitants of the hidden settlement can escape the sufferings wrought by the war.