Nuon Chea, the infamous “Brother Number Two” who presided over some of the worst atrocities of Khmer Rouge rule in Cambodia in the late 1970s and ultimately was convicted of crimes against humanity and genocide, died Aug. 4 at a hospital in Phnom Penh. He was 93.

The country’s U.N.-assisted genocide tribunal confirmed the death but did not disclose the cause.

As the secretive chief ideologue and deputy of the radical communist regime led by Pol Pot, he was the official mainly responsible for devising and operating the Khmer Rouge killing machine — carrying out a policy of mass executions that became a hallmark of Cambodia’s holocaust. It is estimated that about 2 million people died, roughly a quarter of the country’s population, from summary executions, famine, disease and overwork during the Khmer Rouge’s brief but brutal reign of terror from 1975 to 1979.

Known as “Pol Pot’s shadow,” Mr. Nuon Chea was convicted of crimes against humanity by a special U.N.-backed tribunal in 2014 and sentenced to life imprisonment. He was 88, the oldest and most senior surviving Khmer Rouge leader and one of two defendants in the case. Khieu Samphan, the regime’s titular former president, was convicted with him.

After a second lengthy trial, the tribunal in 2018 also found Mr. Nuon Chea guilty of genocide against minority Cham Muslims and ethnic Vietnamese and handed him another life sentence.

According to a notorious former Khmer Rouge security chief and prison warden, Mr. Nuon Chea personally oversaw massive purges of suspected “traitors” within Khmer Rouge ranks. Thousands were tortured into making bogus confessions at the Tuol Sleng prison in the capital, Phnom Penh, and were subsequently executed. At least 14,000 prisoners passed through the former high school’s gates. Only seven survived.

It was Mr. Nuon Chea, not Pol Pot, who directly ordered the killings, the former security chief, Kaing Khek Iev, better known as Duch, told journalist Nate Thayer during interviews in 1999. Duch’s account was supported by documents left behind at Tuol Sleng.

In the regime’s final days before Vietnamese invasion forces captured Phnom Penh in January 1979, Mr. Nuon Chea also “ordered me to kill all the remaining prisoners” at Tuol Sleng, Duch said. Among them were at least two Americans, who were captured while sailing a yacht off the Cambodian coast in late 1978 and tortured into “confessing” that they worked for the CIA.

For some purge victims, Duch recalled, Mr. Nuon Chea demanded that Duch bring photos of their dead bodies to his office to prove they had been executed, Thayer reported in the Far Eastern Economic Review.

Unlike other former Khmer Rouge leaders who were called to account for the regime’s crimes, Mr. Nuon Chea was largely unrepentant.

“Believe me, if these traitors were alive, the Khmers as a people would have been finished,” he said, referring to those purged, in a video recorded by a Cambodian journalist before the former Khmer Rouge second-in-command was arrested in 2007. “So I dare to suggest our decision was the correct one. If we had shown mercy to these people, the nation would have been lost.”

He added: “We didn’t kill many. We only killed the bad people, not the good.” Video clips of his remarks were played at his trial.

Born Lao Kim Lorn on July 7, 1926, in Cambodia’s western Battambang province, Mr. Nuon Chea grew up in a Sino-Khmer family of modest means, the third of nine children. His father was a trader and a corn farmer; his mother was a seamstress. His early education was in the Thai, French and Khmer languages.

In 1942, he traveled to Bangkok in neighboring Thailand to complete high school and pursue higher education. (Thailand took control of Battambang during World War II, making him a Thai citizen.) Using the pseudonym Runglert Laodi, he stayed at a temple with Buddhist monks and attended a school on the premises. Starting in 1946, he studied law at Bangkok’s Thammasat University. He also joined a leftist Thai youth group and worked as a clerk in the Thai Finance Ministry.

In 1950, Mr. Nuon Chea joined the Communist Party of Thailand while still at Thammasat. Later that year, a month after starting a clerical job at the Foreign Ministry, he abandoned his studies, joined the Vietnamese-led Communist Party of Indochina and returned to Cambodia to participate in the struggle against French co­lo­ni­al­ism. He adopted Nuon Chea as his “revolutionary name.”

He made his way to North Vietnam in 1953 and underwent two years of training. He then returned to Phnom Penh, where he met Pol Pot for the first time. In 1960, he was elected deputy secretary of an underground party whose members were dubbed the “Khmers Rouges” (Red Khmers) by Cambodia’s leader at the time, Prince Norodom Sihanouk. It later became the Communist Party of Kampuchea, known as the shadowy “Angka,” or Organization, and unveiled publicly only in 1977.

In a marriage arranged by the party, Mr. Nuon Chea in 1957 wed Ly Kim Seng, who would become a cook for Pol Pot, tasked with safeguarding him from poisoning. She and their four children survive.

When Sihanouk’s government published a list of 34 suspected “subversive agents” in 1963, Pol Pot, who was on the list under his real name, fled the capital with some of his top confederates. Mr. Nuon Chea, whose identity remained secret, stayed behind, working variously as a teacher, food vendor and company clerk while trying to build the party and occasionally traveling in disguise to visit Pol Pot in his jungle hideouts.

Eventually, after Sihanouk was deposed in a 1970 military coup, Mr. Nuon Chea fled Phnom Penh as well. An outraged Sihanouk joined forces with his former adversaries, whose ranks then swelled dramatically. By April 1975, the U.S.-backed government’s forces were spent, and the Khmer Rouge swept into the capital.

Government troops and officials were promptly massacred. Phnom Penh and other cities were evacuated, their residents forced at gunpoint to trek into the countryside to toil in the fields. Disobedience was met with summary execution. The country was transformed into a vast slave labor camp. People, especially city dwellers, were completely expendable. It was all part of a half-baked plan — concocted in the jungles from a toxic brew of Marxism and what one scholar described as “badly digested Maoism” — to create a pure communist state in a single bound.

When it failed, resulting in famine, widespread death and economic ruin, the revolution turned on itself. Mr. Nuon Chea and other leaders blamed internal sabotage, and massive purges were launched.

Driven from power by the 1979 Vietnamese invasion, the Khmer Rouge leadership retreated to western Cambodia and resumed guerrilla warfare. But the insurgency gradually petered out in the 1990s following U.N.-backed elections, and Mr. Nuon Chea formally surrendered to the government in late 1998. He expected to be allowed to continue living modestly next door to Khieu Samphan in the remote Pailin province, but both were arrested in 2007 on charges of crimes against humanity.

At his trial, Mr. Nuon Chea defended the decision to evacuate Cambodian cities, claiming it was to save the population from feared U.S. bombardment and ensure access to food supplies. He blamed Vietnamese agents for virtually everything that went wrong during Khmer Rouge rule.

But prosecutors presented evidence that he had personally ordered torture and executions on a massive scale.

Confessions recovered from the Tuol Sleng prison provided a chilling counterpoint to claims, notably expressed by President Trump, that “torture works.” Instead, they showed that people will say anything under torture to make it stop. Among the torture victims was Hu Nim, Pol Pot’s former information minister, who confessed to being a longtime “officer of the CIA.” He wrote: “I’m not a human being, I’m an animal.” Hu Nim was executed in July 1977, after three months in Tuol Sleng.

In April 1978, two Americans, James William Clark and Lance McNamara, were captured when their boat was fired upon and stopped by Khmer Rouge forces. In a 20-page typewritten confession, Clark spun a bizarre tale of drug smuggling as a cover for espionage. Describing his purported recruitment, he wrote that he signed a paper that “made me a member of the CIA with the number 1492.”

One of the last of four Americans slain at Tuol Sleng was Michael Scott Deeds, who wrote that he was on a spying mission for the CIA when he was caught sailing a yacht with a fellow Californian, Christopher Edward Delance, off the Cambodian coast in November 1978. Deeds, 29, said he joined the Navy at age 18 and, after one week of training, was recruited into the CIA by a man named Lazenby, “a commanding officer of the CIA.” (Actor George Lazenby played James Bond in a 1969 film.) The document was dated Jan. 5, 1979, two days before the Vietnamese captured Phnom Penh.

The voluminous records left behind at Tuol Sleng — including descriptions of torture and photos of victims before and after they were “smashed to pieces,” in Khmer Rouge parlance — constituted a trove of incriminating evidence, and Mr. Nuon Chea was furious with Duch that all of it was not burned before the Khmer Rouge fled.

But Duch had a retort for the furtive Brother Number Two. As he explained years later: “Nuon Chea didn’t tell me the Vietnamese were coming.”