
With this objective Sam storms through Mesoamerica, then travels to Mesopotamia and finally to medieval Europe where the starship is located. 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. However not all is lost, since the Sirians left a back-up ship on Earth. Serious Sam crash lands in Central America in the Mayan age. Unfortunately Sam's vehicle is accidentally hit by the "Croteam crate-bus" and plummets down to Earth's surface. The Second Encounter starts right where the previous chapter left off, with Sam travelling to Sirius on the starship. Sam goes to the Great Pyramid for a rendezvous with the ship and, after a titanic battle against Mental's general Ugh Zan III, he is whisked on-board the Sirian starship.

During his wandering, Sam is able to activate a hidden Sirian communicator, located in Luxor, that summons to Earth a starship from the depths of space.

As the game opens, Sam appears in ancient Egypt: his travels from one Egyptian monument to the next, all the way fighting against the monsters Mental sent after him, make up most of the story of The First Encounter. Because of his bravery in fighting the monsters, Sam "Serious" Stone is chosen to use the "Time Lock". In the 22nd century Mental's forces return to Earth hell-bent on eradicating humankind: as a last resort the usage of the "Time Lock" is decided: this Sirian device can send back through time a single individual who can, hopefully, defeat Mental and alter the course of history. In ancient times, Earth was involved in a conflict between Mental and the Sirians, an alien race that left many of its artifacts to be found by humanity.
