Flight of the Intruder begins with a night attack mission flown by Jake Grafton and his navigator Morgan "Morg" McPherson from the USN aircraft carrier, USS Shiloh, striking a target in North Vietnam. Although there are many militarily valuable targets in North Vietnam, Grafton and other aviators are instead routinely ordered to hit worthless targets—typically "suspected truck parks". The pilots are barred from hitting the more valuable targets because of restrictive "rules of engagement" imposed on American forces. Despite the minimal damage even a successful strike will inflict on the enemy, North Vietnamese airspace is heavily defended, making the missions extremely dangerous for the aviators. Grafton and Morg elude most of the defenses, but a stray shot fired by a lone farmer on the ground fatally wounds Morg. Traumatized by the loss of his good friend, Grafton begins to question whether his efforts have been worth it. He is eventually paired up with Virgil 'Tiger' Cole as his new navigator. Cole, an aggressive veteran with experience over the most heavily defended areas of North Vietnam, becomes aware of Grafton's frustrations, and the two begin to plan an unauthorized mission against a Communist Party center in Hanoi, which will be a serious violation of the restrictive rules of engagement. With the help of one of the Shiloh's intelligence officers, Cole and Grafton locate and plan the mission. Flying the mission nearly proves fatal due to problems with the A-6's weapons system. Once completed, they don't even know if they successfully hit anything. Grafton's superiors soon learn of the unauthorized strike—there is no way to hide the fact that Grafton's plane was shot at by Surface to Air Missiles, yet no SAM sites were positioned near the target they were supposed to hit. Both Grafton and Cole are prosecuted by the Navy, with a conviction being certain. The charges are dropped however, as the Richard Nixon administration is about to authorize a massive new air war campaign against Hanoi, "Linebacker II". The Navy decides that they can't prosecute pilots for flying a mission against Hanoi when the President is about to order an escalation along the same lines. The remainder of the novel follows Grafton's exploits in what became known as The Christmas Bombings. He also romances Callie, his future wife. He is shot down during the offensive, and is forced to confront the horror of war on the ground, and the story closes with Grafton being rescued.
Virgil "Tiger" Cole - An experienced aviator. He has flown in missions over Hanoi at least twice, and his favorite missions are those against missile sites.
Commander Frank Camparelli - The commanding officer of Grafton's A-6 squadron.
"Cowboy" - also a naval aviator. Cowboy will appear in the sequel Final Flight. A man of few words, Cowboy's persona hides a man of above average intelligence.
Morgan "Morg" McPherson; Grafton's navigator and close friend.
"Rabbit" Wilson - A naval aviator with seniority over Grafton, but hobbled by his fear of night flying, which has led to his being mocked by other pilots. Wilson avoids many night missions by "finding" technical faults with his assigned aircraft. Eventually, his "downing" of a night mission aircraft comes to the attention of superior officers. His fate is never specified, though it is presumed that he is removed from flying status.
Aircraft appearing/mentioned
The Grumman A-6 Intruder. A two-man, twin-engine bomber flown from aircraft carriers. The Intruder uses sophisticated electronics to find and attack targets in bad weather and/or at night—though the equipment often proves unreliable. The Intruder also lacks any defensive weapons against fighters.
The McDonnell Douglas F-4 Phantom II, also a two-man, twin-engine warplane flown from USN aircraft carriers. It lacks the sophisticated ground attack capability of the Intruder, but is also more capable than that plane against enemy fighters. An enemy pursuing Grafton is driven off by a Phantom.
The Vought A-7 Corsair II, a simple, one-man, carrier-borne, ground-attack aircraft. Grafton compares his own Intruder to the Corsair, wishing the Intruder were armed with an internal gun like the Corsair was.
Mikoyan-Gurevich MiG-19 Farmer, a twin-engine, supersonic interceptor flown by the air force of North Vietnam. In one mission, Grafton is tasked to attack a group of MiG-19's on the ground. The MiG-19 is derided as a day fighter that would be "mincemeat" if caught in the air by Phantoms.
Video game
Flight of the Intruder, a video game based on the novel, was released for personal computers in 1990 and re-released for the Nintendo Entertainment System around the same time as the film adaptation. Certain boxed copies of the personal computer versions included a copy of the novel as well. Developed by Rowan Software, Ltd. and published by Spectrum Holobyte, the game allowed players the choice of flying either the A-6 intruder or the F-4 from aircraft carriers against targets in the Democratic Republic of Vietnam. Players were challenged both by the comprehensive enemy defenses and the restrictive and complex rules of engagement. Realistic features included unreliable missiles and smokey engines for the Phantom. At lower realism settings, F-4's had missiles and an internal cannon - in contrast to real USN whose F-4's were armed only with missiles.
Sequels
Flight of the Intruder lays the groundwork for other Stephen Coonts novels. In particular, The Intruders, which details Grafton's flying in the immediate aftermath of the Vietnam War, and Final Flight which shows Grafton as CAG of an aircraft carrier boarded by terrorists. In other books, the character of Jake Grafton eventually continues serving the USN into the 1990s, following the collapse of the Soviet Union and Desert Storm. Eventually, he finds himself serving as an assistant to the Joint Chiefs, and is last heard from in the book The Disciple, working for the CIA.