A man walks into a museum for its inauguration and is greeted by Lira, a guide. The main story of Katips is presented as Lira's tour of the museum and as a retrospective narrative written by the museum curator for a book.
In the 1970s, Greg, Panyong, Art, Alet, Estong, and Sussie, all members of various student organizations, host and attend a picket rally, along with members of the Catholic Church, Sr. Claire and Sister Josie. The rally denounces the government of the incumbent Philippine President, Apo (an allegory for Ferdinand Marcos), and marks the opening stage of the First Quarter Storm. Ka Manding arrives at the rally after a meeting where demands such as a non-partisan constitutional convention are stated. He mentions his daughter who is returning to the Philippines from the United States after the death of her mother. A team of METROPOL soldiers led by Lieutenant Sales arrive at the rally, arresting Ka Manding for sedition and rebellion. While driving away, they strangle Ka Manding and, after ensuring there are no witnesses, throw his body down a cliff. The soldiers later return at night, beating the protesters with batons and blasting them with high-pressure water from a fire truck.
Some time after Martial Law is imposed, Lara meets the daughter of Ka Manding at the University of the Philippines. They collect some of Ka Manding's personal belongings from his apartment and head to a safe haven for students who were still outside past curfew: the Katips house, operated by Alet. Meanwhile, Art, the photographer of the Philippine Collegian, introduces Lally to the writers of the paper, consisting of Bebang, Sussie, and Panyong, who also works as a writer for Ang Bayan, the newsletter of the Communist Party of the Philippines. With the curfew nearing, the writers rush home. While making his way to the Katips house, Panyong narrowly escapes capture from METROPOL officers. After [Panyong] rants about American influence on the Philippines, Lara enters a heated discussion with him, defending the imposition of martial law and showing support for Apo. Meanwhile, Art introduces Lally to his father, Mang Temyong, a supporter of Apo and a Metro Manila Aide who sweeps the streets of Manila to appease Imelda. [Alet], after fighting with Lara about their differing perspectives on life as a Philippine citizen, tells the story of her love interest, Ben, a desaparecido who disappeared after attending a mass action protest. They then explain the death of Ka Manding to Lara, who joins their cause.
The main cast assemble again in front of a distillery, La Disilleria, to protest unfair labor practices. During dinner, Alet touts [Panyong] for being numb toward her; Panyong defends himself and admits his love for her. The following day, METROPOL officers arrive at the protest, again assaulting demonstrators and arresting Art and Estong. The protesters are distraught at the encounter, which left the two arrested missing as they could not be found in nearby precincts. Some time later, [Panyong] and Greg begin packing to return to the mountains as guerrilla soldiers of the New People’s Army. [Alet] is kidnapped by a METROPOL soldier and brought to a torture house. Art and Estong are both shown being brutally tortured by METROPOL officers; they are burned by cigarettes and flat irons, made to sit on ice blocks, have nails removed with pliers, are urinated on, and electrocuted. [Alet] is beaten by [Lt. Sales], who reveals that Ben is alive and that he had betrayed her as part of his job. [Alet] is raped by [Lt. Sales], and all three captured are shot dead. After learning of the discovery of her mutilated corpse, Greg leads [Panyong] to her body, which is found at the side of a river. [Panyong] swears revenge against the perpetrators and heads to the mountains with Greg. Years later, during the People Power Revolution, Lara takes [Alet]’s place as the caretaker of the Katips house. As she reads from the Malaya that Greg and [Panyong] had died, Greg, who had been mistakenly presumed dead, returns home to her and their son, Greggy.
At the present day, Greggy is revealed to be the museum visitor and a lawyer for Claimants 1081, an organization of martial law victims. [Panyong], also mistakenly presumed dead, is the museum curator. The student activists of the 1970s, now elderly, arrive at the inauguration of the Bantayog ng mga Bayani, dedicated to the victims of human rights abuses during martial law.
