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.
Per Rolling Thunder, the strength and attack patterns of the standard enemy soldiers that the player will face is determined by the colors of their outfit,[4] and "strange" enemies such as Snipers, Frogmen, and Maniacs appear later on.[5][6] There are a total of eight stages, with three difficulty settings.