The Second Encounter starts where the previous episode 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 that of Sam, the hero has to uncover the locations of a number of Sirian time-gates that will help him reach his destination. With this objective, Sam storms through Ancient Mesoamerica, then travels to Ancient Mesopotamia and finally to Medieval Europe where the starship is located.