Code Name: Viper

The gameplay system is similar to Namco's 1986 arcade game Rolling Thunder, specifically its own NES version. Like in Rolling Thunder, the player can jump or drop down between floors by holding the directional pad up or down and pressing the jump button, as well as enter doors to obtain power-ups or avoid enemies. The player can be armed with one of two weapons (a standard issue pistol or a fully automatic machine gun for continuous firepower). Items includes additional ammunition for either weapon, extra health, a time extension, and extra lives. Unlike Rolling Thunder, the player can shoot while jumping and can also change directions during midair.

Another difference between Rolling Thunder and Code Name: Viper is the added emphasis on rescuing hostages, like the also-similar Shinobi. Throughout the first seven stages, the player can find captured civilians, who will offer the player their gratitude, behind certain doors. To complete each of the first seven stages, the player must rescue a captured commando who will provide the grenades necessary to blow up the obstruction blocking the exit at the end of each stage and advance the plot. At the end of each stage, Kenny will be seen at a campfire with the rescued commando, who will provide clues which is then shown in a blank letter that slowly starts to gain words and outline.

The player takes the role of Kenny Smith, code name "Viper", an agent of the 98th Special Forces. He is assigned by his superior, Commander Jones, to investigate a large drug syndicate that covers most of South America (Venezuela, Brazil, Chile, Peru, Paraguay, Argentina, Bolivia). Smith's objective is to rescue a missing agent in each of the syndicate's seven hideouts and uncover clues of the Syndicate's true mastermind.