Operation Stealth mainly features a point-and-click style of gameplay reminiscent of many of the LucasArts adventures of the time, as well as a number of more action-oriented elements, including an overhead viewed maze section and a scene in which Glames/Bond attempts to escape from an underwater cavern before he runs out of oxygen.

The crack featured a bug which meant that if the player attempted to click the mouse button in order to skip through the speech faster the game would freeze and have to be rebooted.

John Glames (James Bond in the U.S.), a CIA secret agent, has been assigned a mission to locate a newly designed high-tech F-19 type stealth plane in Latin America, which was stolen from NAS Miramar.

The protagonist visits the banana republic of Santa Paragua to investigate; upon meeting his contact, the agent is apparently assassinated and hands Glames the key to a bank slot where the case documents are kept.

Once he retrieves an envelope, it turns out that the man he met was Colonel Karpov of the KGB; he explains that they captured the CIA contact and manipulated Glames to open his briefcase as he would know the combination.

Inside, the chief debriefs him and explains that the Stealth fighter was stolen by the global criminal/terrorist organization Spyder led by Dr. Why and threatens to attack major cities around the world.