The Second Encounter starts where the previous chapter left off, with Sam travelling to Sirius on the starship. Unfortunately Sam's vehicle is accidentally hit by the "Croteam crate-bus" and plummets down to Earth's surface. Serious Sam crash lands in Central America in the Mayan age. However not all is lost, since the Sirians left a back-up ship on Earth. Since this vehicle is located in a different age from the one Sam finds himself, the hero has to uncover the locations of a number of Sirian time-gates that will help him reach his destination.