(as given by Nintendo)

High above New York City a helicopter explodes. Aboard the craft is the latest biological warfare weapon which has been secretly developed by the CIA (Central Intelligence Agency)... Cassandra-G. A vaccine and plans have been stolen are among the fragments of the helicopter wreckage along with a shell fired from an M16.

The copter was shot down from fire of an expert sharpshooter armed with an M-16. The CIA concludes that the act was the responsibility of the super sniper, Golgo-13. An official release by the CIA links Golgo-13 to the KGB (the Soviet intelligence group).

Under these circumstances, The CIA copter incident and the unknown where-abouts of Cassandra-G become entangled. A representative of the secret international organization, FIXER, transmits a message. FIXER believes the affair is the work of the remnants of the DREK Empire and not Golgo-13.

After the dispatch, the representative disappears. The situation becomes more and more mysterious. A man who calls himself Condor agrees to help FIXER. In East Berlin, because Condor has received some information on Cassandra-G, the CIA, KGB, and even DREK are threatening his life

Upon a request from FIXER, Golgo-13 has gone into action. He is to get information on a vaccine from Condor and eliminate the leader of the DREK group...

At the time, Nintendo of America had strict censorship policies concerning what sort of content could be depicted or referenced in any game published for a Nintendo system. In the original Japanese version, the DREK "empire" is actually the resurrected Nazi regime, but this was changed so as to fit the prohibition against political advocacy, racial and or ethnic stereotyping.

Yet, some of the changes were more complete than others. The final boss, Smirk, is clearly a cyborg version of Adolf Hitler and a file retrieved by Togo during a base infiltration in Greece retains a swastika on it, which is visible in the player's inventory area. Nintendo required that Golgo had his profession changed to spy rather than assassin, per its prohibition on graphic violence and gore.

Golgo 13 is one of the first NES games to feature sex, drug use and graphic violence. It was an unusual release, because at the time Nintendo of America had strict content guidelines preventing the release of such content on its systems. Although the depictions were toned down from the original Japanese counterparts and limited by the 8-bit technology of the NES, it was not all together clear how this content was released uncensored.

For example, in the maze levels featured in the game, as well as one "sniper mode" mission in East Berlin, enemies are seen briefly bleeding from the head when killed, despite the prohibition on graphic violence and gore.

In the beginning of the mission in Greece, if the player walks to the right several paces and then walks back to the beginning of the level, a pack of cigarettes is seen on the ground. Golgo 13 is seen smoking if the player walks over the cigarettes, and his health is restored.

The Japanese version even had an alternate sequence (prompting the player to "press the B button and have the kids look away from the screen") which had Cherry remove her dress leaving her dressed only in panties for a few seconds.

In the sequel, The Mafat Conspiracy, scenes are even more 'graphic' taking into consideration the technology of the time.

• Duke Togo (Golgo-13) - Uses a custom-made M-16 regularly, a sharpshooter with 100% accuracy, the ultimate sniper. His details are shrouded in secrecy. Dragged into the scene when a CIA chopper explodes and goes down, he now undertakes to solve the whole mess as requested.
• Cherry Grace - Dispatched from FIXER, she is assigned to assist Golgo-13.
• Condor - Because he has acquired information on Cassandra-G, the CIA, KGB, and DREK are after him.
• Oz Windham He is a FIXER investigator whose whereabouts are currently unknown. He is being held prisoner in the underground base of the DREK group somewhere in East Berlin.

Golgo 13's energy level starts at 200 and continuously declines. Destroying enemies increases his energy level and bullets. The game consists, chronologically, of 13 acts (all named for classic films):

• Act 1 — The Iron Curtain
• Act 2 — The Moving Target
• Act 3 — River of No Return
• Act 4 — A Farewell to Arms
• Act 5 — Spartacus
• Act 6 — The Third Man
• Act 7 — Sleeping Beauty
• Act 8 — All About Eve
• Act 9 — Apocalypse Now
• Act 10 — From Here to Eternity
• Act 11 — The Godfather
• Act 12 — In the Twilight
• Act 13 — And There Were None

One of the most challenging aspects of the game is that these acts are intended to be played out as though they were a limited number of episodes in a television series, or perhaps as issues in a limited series comic book since the game's title character originates in Japanese manga. The game only lasts fifty-two episodes, meaning the player only gets fifty-two chances to beat the game. Episodes begin at one and are counted upward from the start screen each time the player loses a life. At the end of the fifty-second episode the game resets and begins again from the main title screen. In video game jargon, this is to say that the player has a maximum of fifty-two "lives" to complete all thirteen acts before the game resets.

• Golgo 13
• The Mafat Conspiracy