Equilibrium is set in 2072 in Libria, a city-state established by the survivors of World War III, which devastated the world, where a totalitarian government requires all citizens to take daily injections of "Prozium II" to suppress emotion and encourage obedience. All emotionally stimulating material has been banned, and "Sense Offenders" – those who fail to take their Prozium – are put to death, as the government claims that the cause of all wars and violence is emotion. Libria is governed by the Tetragrammaton Council, led by "Father", who is seen only on giant video screens throughout the city. At the pinnacle of Librian law enforcement are the Grammaton Clerics, who are trained in the martial art of gun kata. The Clerics frequently raid the "Nether" regions outside the city to search for and destroy illegal materials – art, literature, and music – and execute the people hiding them. A resistance movement, known as the "Underground", emerges with the goal of toppling Father and the Tetragrammaton Council.
John Preston (Christian Bale) is a high-ranking Cleric. His wife, Viviana (Alexa Summer and Maria Pia Calzone), was executed as a Sense Offender. Following a raid, Preston notices his partner, Errol Partridge (Sean Bean), saving a book of poems instead of turning it in for incineration. Preston tracks down Partridge, who is hiding in the Nether region reading the book. Partridge confesses to Preston that he believes he was wrong to serve the government. He acknowledges that the consequences of feeling emotions are a "heavy cost", but remarks, "I pay it gladly" as he slowly reaches for his gun. Preston is forced to execute him.
Preston dreams occasionally about his wife and the day she was arrested. After Preston accidentally breaks his daily vial of Prozium, his son Robbie enters and reminds him that he needs to report the loss and request a replacement, but Preston is unable to before going on the next raid. As a result, he begins to experience brief episodes of emotion that evoke memories, stir feelings, and make him more aware of his surroundings. He intentionally skips more doses of Prozium and hides them behind the mirror in his bathroom.
Preston's partner is replaced with career-conscious Brandt (Taye Diggs), who expresses his admiration for Preston's "uncompromising" work as a cleric. On their first raid, they arrest Mary O'Brien (Emily Watson), a citizen identified as a Sense Offender. To Brandt's surprise, Preston prevents him from executing O'Brien on the spot, saying that he wants to keep her alive for interrogation. Brandt grows suspicious of Preston's hesitation to execute Sense Offenders and destroy contraband. As a result of his new secret emotions, Preston feels remorse for having killed Partridge, and he also develops an emotional relationship with O'Brien. Preston eventually uncovers clues that lead to a meeting with Jurgen (William Fichtner), the leader of the Underground resistance. Jurgen convinces him that Father must be assassinated. They plan to disrupt Prozium production in an attempt to spark a popular uprising.
Preston is brought before Vice-Counsel DuPont (Angus Macfadyen), who reveals that there is a traitor in the upper ranks of the Clerics. DuPont appears to be onto Preston, but then assigns him the task of uncovering and stopping the traitor. Relieved to learn he has not been implicated, Preston accepts and renews a promise to locate the Underground's leadership. He learns of O'Brien's scheduled incineration, but Jurgen advises against interfering, which could sabotage plans for the revolution. Jurgen decides to allow the leaders of the resistance to be captured by Preston, so that Preston can gain the government's trust in order to approach Father and assassinate him. Preston rushes to stop O’Brien from being executed, but his efforts are in vain and she is incinerated right in front of him. Brandt catches Preston having an emotional breakdown in the streets, arrests him, and brings him before the Vice-Counsel. Preston tricks DuPont into believing that Brandt is the real traitor. Following Brandt's arrest, Preston is informed that a search of his home will take place as a formality. He rushes home to destroy the hidden vials, only to find his son – who along with Preston's daughter, stopped taking Prozium after his mother died – already has. Preston turns in Jurgen and others from the resistance, and as a reward, is granted an exclusive audience with Father. Upon arriving, he discovers that Brandt was not actually arrested but was part of a ruse to expose Preston and the Underground. DuPont is also revealed as the real Father; he had secretly replaced the original Father after his death. It also becomes clear that DuPont does not take Prozium and can feel emotions. He taunts Preston, asking him how it felt to betray the Underground. Enraged, Preston fights his way through an army of bodyguards into DuPont's office and defeats Brandt in a katana battle. In a final gun kata showdown with DuPont, Preston wins. DuPont pleads for his life reminding Preston that he represents life and feeling and asks, "Is it really worth the price?" Preston has a flashback of O’Brien in the furnace, and then responds with Partridge's last words, "I pay it gladly" before shooting DuPont and destroying
the command center that broadcasts propaganda videos of Father. The Underground carries out the destruction of Prozium manufacturing and storage facilities and attacks key points throughout the city. Preston watches the successful revolution with satisfaction from above in DuPont's office, as a smile breaks across his face.