While there is no "CIA" faction within the Metal Slug games, the series heavily utilizes the concept of clandestine intelligence agencies through its own fictional organizations. The Intelligence Agency (Regular Army)

The "Prisoner of War" Paradox

A curious element that fuels the CIA legend is the treatment of Prisoners of War (POWs). Throughout the levels, players rescue one-eyed soldiers who offer weapons and items. These prisoners are emaciated, bound, and often hidden in walls or under floorboards.

Metal Slug: CIA — Complete Write-up

Overview

Metal Slug: CIA is a fan-made, noncommercial expansion/translation project built around the classic Metal Slug run-and-gun arcade series originally developed by SNK. The project name typically references a ROM hack or translated release intended to run on hardware or emulators that play Neo Geo / Neo Geo Pocket / other platform ROM images. It combines the series’ trademark fast-paced side-scrolling shooter gameplay with new or altered content—such as modified levels, enemy placements, difficulty tuning, bug fixes, and localization changes—while keeping the core Metal Slug mechanics intact: responsive run-and-gun action, vehicle (Slug) sections, and over-the-top enemy designs.

There is no official connection between the video game franchise and the Central Intelligence Agency (CIA). Instead, users often search for "Metal Slug CIA" when looking for game files to install on custom-firmware Nintendo handhelds. The Metal Slug Series: A Brief Overview