Parris Island, South Carolina, U.S. Marine Corps Training Camp: late 1960s. A group of young Marine recruits, their heads shaven and their identities erased, are prepped for basic training to become Marines. They are subjected to the brutal Gunnery Sergeant Hartman (R. Lee Ermy), whose orders are to "weed out all non-hackers." Hartman gives each of the Marines nicknames by their posture and response, naming one pragmatic recruit 'Joker' (Matthew Modine) for talking behind his back, another recruit is 'Cowboy' (Arliss Howard) for being from Texas, and a 6'3", 280-lb recruit, named Leonard Lawrence (Vincent D'Ofrio), is nicknamed 'Gomer Pyle'.
Gomer Pyle becomes the subject of Hartman's brutality because the recruit is merely a slow-witted, overgrown boy with no intelligence or ambition. The overweight Pyle just cannot keep up with the other fit recruits in the grueling obstacle courses.
One morning when Hartman asks Joker if he belives in the Virgin Mary, Joker responds that she doesn't, angering the drill instructor. The clearly religious Catholic Hartman contines to ask Joker if he belives in the Virgin Mary, but Joker talks back confirming that he doesn't and that he's an atheist. Despite Hartman slaping Joker in the face, Joker stubborly refuses to reverse his answer, which makes him a quick hero to the other recruites standing beside him. But Hartman immediately turns Joker from hero to outcast by giving Joker the unpopular job of being the squad leader and also gives him the difficult job of being Pyle's personal instructor. Over the next few days, off on the sidelines, Joker shows Pyle how to operate and clean a rifle, make and fold bed sheets, and helps him through the obstacle courses.
But one evening during a routine inspection, Hartman notices that Pyle's foot locker is unlocked and upon searching it, finds a jelly donut in Pyle's foot locker. Enranged, Hartman decides that from now on instead of punishing Pyle for it, Hartman punishes the entire barracks as an example. That night, the recruits decide to give Pyle a red alert: while Cowboy and a few others hold Pyle down in his bed, the recruits attack the fat recruit with soap bars wrapped in towels. Joker is at first reluntantly to attack his friend, but after being persuaded by Cowboy, Joker hits Pyle longer and harder than most of the recruites.
After this Pyle begins to go slowly insane from this traumatic experince. But he not only shapes up but he becomes the fastest and quickest rifleman of the entire platoon which impresses Hartman. But Joker sees Pyle is losing his true human self when he sees Pyle talking to his rifle, and begins stairing off blankly. Joker confides in Cowboy about Pyle's growing mental problems. By the end of basic training, Pyle clearly has been completely dehumanized by the rigors of basic training.
On the last night at Parris Island, Joker is doing fire watch when he runs into Pyle in the barracks latrine loading life rounds into his rifle. Pyle, now completely psychotic, yells command orders which awakens Hartman who enters the latrine and orders him to put down the rifle. Pyle responds by killing the drill instructor. Then Pyle turns the rifle on himself and fires.
Da Nang, Vietnam. One Year Later. Joker is now a reporter for the Stars and Stripes, a Marine Corps newspaper detailing the war in Vietnam. With his partner, combat photographer Rafterman they meet a local prositute in the streets, and have an encounter with a local thief who steals Rafterman's camera. Upon arrival back at their base, they are given assignments while Joker still resents not being able to get out in the country and get a good story. But that night, January 31, 1968 just after midnight, the Tet Offensive strikes. The NVA assault against the Marine Corps base at Da Nang is easily beaten back.
The next morning, Joker and Rafterman are assigned to cover the fighting in Hue which has been seized by NVA communists. Joker and Raferman fly to out Pu Bai and meet Joker's basic training friend, Cowboy, leading a platoon to recapture the south side of Hue. Going through a battle, the GI grunts give their own opinions about the fighting and insanity of the war.
A few days later, Joker and Rafterman accompany Cowboy and a squad into the ruins of the south side of Hue after an NVA pullout. But the squad wanders off too far and they soon find themselves pinned down by an unseen sniper in a cluster of buildings. One grunt, Eightball (Dorian Harewood), is hit and another, Doc Jay (John Stafford), is also hit and killed when he tries to drag Eightball to safety. One big grunt, Animal Mother (Adam Baldwin), disregards orders to pull out and locates the sniper, but Cowboy is hit while trying to rally his men. The grunts split up and search the building with the sniper in it. Joker locates the sniper, an NVA woman, who nearly kills him, but he is saved by Rafterman who shoots her.
With the grunts looking down at their dying enemy, Joker suggests they can't leave the sniper like this and he shoots her, out of both compassion and revenge. Afterward, the squad meets their main unit and heads out, as the aetheist Joker comments, "I am in a world of shit, but I am alive and I am not afraid."
