After taking part in an initiation rite on his first crossing of the Equator, Darwin reaches South America. There he finds the wonders of the Brazilian rainforest. During a stay in Rio de Janeiro he is confronted by the horrors of slavery.

The Beagle lands on Tierra del Fuego the southernmost tip of South America. The attempt to place a missionary among the indigenous people there fails.

With the length of the expedition increased, Darwin makes an excursion across Patagonia to Buenos Aires. Later, arriving in Valparaíso, he travels across the Andes.

After finding fossilized sea shells high in the Andes, Darwin returns to the Beagle to find FitzRoy suffering from depression. While in Valparaíso, Darwin experiences earthquakes and their devastating effects. After FitzRoy's recovery, the Beagle travels to the Galápagos Islands where Darwin finds startling revelations.

Darwin studies the finches in the Galápagos that would influence his theories for years to come. The Beagle returns to England after five years at sea. He begins to develop his thoughts based on his discoveries during his travels.

Darwin becomes worried about loss of reputation and public censure of his ideas and delays publishing his work.