The Second Encounter starts where the previous game left off, with Sam traveling to Sirius on the SSS Centerprice. Unfortunately, the starship is accidentally hit by the "Croteam crate-bus" and plummets down to Earth's surface. As the starship falls, Sam reads the coordinates and frets about crash-landing into Egypt again, but instead he crashes into Central America in the Mayan age, with the starship now heavily damaged upon impact. However, not all hope is lost, since the Sirians left a "back-up starship" on Earth, which was a fail-safe in case anything ever happened to the SSS Centerprice. However, since this back-up starship is located in a different time and age than where and when Sam currently is, he will have to uncover the locations of the Sirian portals that will help him reach his destination.