Area 88 takes place in the late 1970s/early 1980s and is largely set in a war-embroiled Middle Eastern country called the Kingdom of Asran. The war uses mercenary fighter pilots, with its headquarters at a secret desert air force base called Area 88. Up-and-coming airline pilot Shin Kazama gets tricked into signing up by his "friend" Satoru Kanzaki. Facing execution for deserting from Area 88, Shin reluctantly turns into a fighter pilot and attempts to serve his three year contract out.
Area 88 attracts all kinds of people with all kinds of assorted and often sordid pasts. Among the other mercenaries are Mick Simon, an American who couldn't adjust to normal life after his tour of duty in the Vietnam War. Mick becomes Shin's best friend at Area 88. Another familiar sight at Area 88 is McCoy, a greedy weapons dealer who sells everything the mercenaries need from toilet paper to the planes that the mercenaries fly in battle. The commander of Area 88 is Saki Vashutal, who is actually a prince of the nation of Aslan, though his royal heritage means nothing there. Also prominent on the base are the war photographer Rocky (presented as Makoto Shinjou in the 2004 anime), the Dane Greg Gates (later featured in the video game adaptation) and the numerous pilots with whom Shin flies (most of whom die over the course of the series, often in the issue in which they were introduced). Though the series focuses mostly on Shin, other characters (notably Rocky and Mick) did have their own individual storylines.
There are only three ways to leave Area 88: Survive three years (highly unlikely), buy out your contract for one and a half million dollars (difficult as a mercenary must pay for all his expenses including stiff fines for turning down hazardous missions) or desertion (a capital offense if caught). With each enemy plane brought down, Shin faces his shifting acceptance of the violence and killing that fills every day, as well as suppressing his feelings of wrong-doing. Eventually earning his release after numerous setbacks, he returns to normal life only to discover he has changed and can no longer fit into the life he once knew.