The game begins in 2025. As time passes, maintaining a full scale military becomes a burden. In a globalized world, the only security threat is from small scale rogue organizations against whom large forces are useless, and the fuel needed to supply increasingly mechanized armies becomes more costly.

Set at an undisclosed date somewhere in Malaysia, NATO Operations Commander Cullen Gray arrives at a NATO operations command center at the request of Area Commander Gorman.

Unit 13 plays much like the SOCOM franchise. The camera stays directly behind the player character in third-person, or otherwise shifts to first person aim if the player selects the option to zoom in with guns that have the compatible attachments.