Serious Sam: The Second Encounter is a shooting game, controlled by the player. The game continues from where the previous game had been left, featuring Sam travelling to Sirius using SSS Centerprice. But to the misfortune of Sam, the starship crashes down and Sam finds himself landed in Central America. The starship is seen highly damaged due to collision.

The main aim of the character in the game is to find an alternative starship, which has its location in a different age and time. It is during this period that Sam has to face various threats and ultimately needs to protect himself. The player acting as Sam needs to fight various monsters using weapons; the game also has a rising storm, which also needs to be survived by the player. The game has certain new weapons like, a flamethrower, a sniper rifle and a very powerful bomb.

Here Sam is seen to face a dozen of new monsters, and the action between the two is even more interesting. Serious Sam: The Second Encounter also sees the introduction of a fan made level named as Dark Island. The concept of the game is new and innovative, and attractive to game lovers of all age.