Set in a British independent boys boarding school in the late 1960s (most of the scenes were filmed at Cheltenham College in Gloucestershire, with the remainder at Uppingham School in Rutland and Aldenham School in Hertfordshire, England, UK). Mick Travis (Malcolm McDowell) is one of three non-conformist boys among the returning class. They are watched and persecuted by the "Whips", senior boys given authority as 'prefects' over juniors. The prefects are entitled to the services of "Scum", who are first-year boys assigned to run errands, make tea and generally act as unpaid servants. This refers to the old tradition of "fagging" which still persisted in many British independent boys' schools.
The early part of the film shows scenes in the school as the pupils return at the start of a new term. Mick Travis, the protagonist, arrives with a suitcase on his shoulder, wearing a black Derby hat, with a black scarf across his face to hide his moustache. Stephans comments, "God, it's Guy Fawkes back again", hinting at the conclusion of the film. Rowntree (Robert Swann) is the Head Whip, and he revels in his power, ordering the junior boys to "Run! Run in the corridor!"
After the first evening meal, the Whips conduct some of the more mundane business of the school, signing up boys for "Confirmation class" and "VD clinic". Each boy has to lower his pants so the school nurse can inspect his genitals.
These early scenes show the school's customs and traditions. The Headmaster (Peter Jeffrey) is somewhat remote from the boys and the House Masters. Mr. Kemp (Arthur Lowe), the House Master to Mick's dorm, is told "I'll have to get back to you on that" when he brings things to the Headmaster's attention. Kemp himself is easily manipulated by the Whips into giving them a free hand in enforcing discipline. Some of the staff are shown as suffering from various perversions. For example, the school chaplain (Geoffrey Chater), who is also the geometry master, enjoys grasping the boys and hurting them during class. At bedtime, Mr. Kemp sings a hymn as his wife (Mary MacLeod) accompanies him on the recorder; the matron (Mona Washbourne), overhearing, is driven to near orgasm. Mrs. Kemp herself enjoys walking naked through the boys' dormitory and washroom while fondling soap, towels and other objects the boys have carelessly strewn about.
One day, having sneaked off campus and into the nearby town (an act strictly forbidden by house rules), Mick steals a motorbike from a showroom and has an affair with a local waitress. Meanwhile, Wallace finds adolescent romance with Bobby Philips, a junior boy, whom he takes to bed. They indulge in self-inflicted ordeals, such as seeing how long they can hold a plastic bag over their faces.
As the film progresses, it concentrates on Mick's group and their clashes with the school authorities. Mick and his friends are subject to punishments, and eventually they are sentenced to corporal punishment in the form of a severe "beating" (i.e. a caning) by the Whips. The caning is administered by Rowntree in the gym with a long run-up. The three boys are left with bleeding buttocks. Mick's punishment is especially brutal (10 strokes), yet tradition demands that he shake hands when it is over and say, "Thank you".
(Note: scenes are shot through with surreal elements, such as some scenes being shot in black and white. This was not for dramatic emphasis, as people presumed, but simply because the huge windows at the college gave off obstructing light that affected the camera lenses. Another explanation given later by Lindsay Anderson is simply that the production was running out of money.)
A few days later, during a paramilitary exercise training in the nearby woods, Mick and his friends play a practical joke on the Whips by planting a bomb containing paint which they detonate and humiliate the Whips and the supervisors of the military exercise. As a result, Mick and his friends are punished by being forced to clean up the church basement for the weekend. During the cleaning, Mick and his group find a large cache of various weapons dating back to the second world war (rifles, heavy machine guns, sub-machine guns, pistols, grenades and even mortar tubes with live rounds). Mick decides to use this to get revenge against the establishment for their misfortune.
At the climax, in a surreal sequence, on Founders' Day, when parents are visiting the school, Mick and his group start a fire under the hall, smoke out the parents, staff and boys, and open fire on them from a rooftop. Led by the visiting General who was giving the speech, the staff and boys break open the Combined Cadet Force armoury and fire back.
The Headmaster tries to stop the firefight and calls for peace. Mick's girl, who is on the roof with them, produces a Webley Revolver from her belt and shoots the Headmaster through the forehead in cold blood. As the battle continues, the camera closes in on Mick's face as he defiantly keeps firing, ending the film with a fade-out and an echo of gunfire with the film's title "if...." emblazoned in red on the screen.