The gameplay consists of a single game type, single- or multi-player, in which the player fights through waves of zombie-like monsters (or more precisely, specimens from a failed military experiment), with each wave becoming successively more difficult, moving through each area of the level, until it concludes with a battle with a super-specimen, called the Patriarch. Alex Quick, the level designer and texture artist, has stated that "there are a whole bunch of ideas on the drawing board that we can add in after launch, including the 'Story' mode from the mod, for instance."

Levels are completely non-linear and open-ended. There are no restrictions on where players can travel—that is, players can choose where to run and fight. Up to six players can team up in an online cooperative battle with the specimens. The game sessions are fully-configurable, so players can change the difficulty, number of enemy waves, or specify which creatures compose the waves. As the player progress through waves, the tougher-grade specimens are more commonly encountered. A Software Development Kit (SDK) and level editor is included to aid in the creation of modifications and levels.

There is an array of weapons, including melee weapons, shotguns, rifles, sidearms and other weapons. Players must earn cash from killing specimens to buy these from the Trader who sells weapons, supplies, and ammo players will need to progress through each wave, who is only accessible after completing a wave. When the next wave begins, she relocates, and near the completion of a wave, a red arrow appears on screen, directing the players to the Trader's new location. Players can also drop cash for other players to collect and spend.

The Protector centres on the exploits of two vastly different characters – hardened British mercenary Jonathan Kane and beautiful US archaeologist Jennifer Guile. After an acrimonious two-year estrangement, these two former lovers are reunited when Jennifer’s father – a leading archaeologist – is murdered by a new terrorist organisation called Scarlet Vengeance, which is looking for a powerful Aztec artefact to use for a devastating terrorist attack. When Scarlet Vengeance’s attentions turn to Jennifer – the only person who knows the location of the artefact – Kane is forced to track her down and protect her. Thrown together in extreme circumstances, the duo must overcome their differences and use their unique skills to thwart the terrorists’ horrifying plan.