On an early April evening 20 years ago, an airplane carrying the president of Rwanda was mysteriously shot down, and the small Central African country launched itself into a killing spree that would last 100 days. Rwanda's genocide was shocking: close-quarter, hand-to-hand butchery, mostly with machetes and other implements. Some 800,000 people were murdered after members of the country's Tutsi minority were targeted by members of its vast Hutu majority.

As Rwanda has sought to rebuild from the ashes of the genocide, the U.S. has felt a special obligation to the victims. During the early weeks of the slaughter, when foreign intervention had the best chance of halting the bloodshed, President Bill Clinton's administration carefully avoided designating the crisis a genocide so as to duck involvement. (When President Clinton visited Rwanda in 1998, he said that the U.S. "did not act quickly enough after the killing began.")

On an early April evening 20 years ago, an airplane carrying the president of Rwanda was mysteriously shot down, and the small Central African country launched itself into a killing spree that would last 100 days. Rwanda's genocide was shocking: close-quarter, hand-to-hand butchery, mostly with machetes and other implements. Some 800,000 people were murdered after members of the country's Tutsi minority were targeted by members of its vast Hutu majority.

As Rwanda has sought to rebuild from the ashes of the genocide, the U.S. has felt a special obligation to the victims. During the early weeks of the slaughter, when foreign intervention had the best chance of halting the bloodshed, President Bill Clinton's administration carefully avoided designating the crisis a genocide so as to duck involvement. (When President Clinton visited Rwanda in 1998, he said that the U.S. "did not act quickly enough after the killing began.")

But today's Rwanda—led by PresidentPaul Kagame, who rose to power as the head of a Tutsi insurgency driving back the Hutu killers in 1994—no longer follows a simple narrative of victims and perpetrators. The longer the U.S. has been guided by that narrative—atoning, in effect, for shirking global leadership during one of the worst mass slaughters of the past century—the more it has become complicit in crimes and misdeeds in Rwanda ever since.

A pattern of U.S. indulgence was established in the earliest days of the post-genocide period, when Mr. Kagame was establishing his authority throughout the country. During those first months, Mr. Kagame's army, composed almost entirely of minority Tutsi, conducted its own mass slaughters across Rwanda, rounding up unarmed Hutu civilians by the thousands and machine-gunning them. These acts were documented at the time by international human rights workers and U.N. experts on the ground. The Kagame government has bristled at accusations of human rights abuses, saying it acted on behalf of the victims of the genocide. (The Rwandan government did not respond to repeated requests for comment on this article.)

A seasoned U.N. investigator, Robert Gersony, estimated that as many as 35,000 Hutu were killed in this manner between April and September 1994 in the 28% of the country that his team surveyed. "What we found," an investigator who took part in the survey told me, "was a well-organized, military style operation, with military command and control, and these were military campaign style mass murders." But the U.N. never released the report. Human Rights Watch reported that the U.S. "concurred in this decision, largely to avoid weakening the new Rwandan government."

Many historians of Rwanda say that this set a powerful precedent of impunity for the new Kagame regime—and paved the way for larger crimes.

Mr. Kagame moved to consolidate his power, with U.S. and other foreign aid accounting for virtually all of the country's budget in 1995. (That figure stands today at 40%, according to the World Bank.) He quickly set about eliminating sources of opposition and criticism throughout Rwanda. Under his rule, independent-minded journalists were jailed or chased into exile. In 1997, Appolos Hakizimana, the editor of a magazine that had criticized the Rwandan military, was shot dead by unidentified gunmen. Rival political leaders (such as Pasteur Bizimungu, the titular but largely powerless president in the late 1990s, and Victoire Ingabire in the last election) were imprisoned; some rival parties have been banned.

Meanwhile, with tacit U.S. support, Mr. Kagame launched a pair of wars against neighboring Zaire (later renamed the Democratic Republic of Congo). The rationale for the first of these conflicts, in 1996, was that Zaire harbored thousands of armed perpetrators of the Rwandan genocide who were bent on revenge. But Mr. Kagame went beyond hunting downgenocidaires, and Rwandan intervention in Congo became habit-forming, at a devastating cost in human lives.

The International Rescue Committee estimates that more than five million people have died since 1998 as a result of the wars and campaign of destabilization waged by Mr. Kagame in Congo. Perhaps the most troubling fact of these conflicts has been Rwanda's pursuit of coldblooded ethnic revenge. Congo has repeatedly accused Rwanda of interference in its affairs; Rwanda says Congo's weak government has done too little to root out Hutu extremists who took part in the 1994 genocide.

In 2010, an exhaustive U.N. report on a decade of Rwandan-sponsored conflict in Congo revealed that Mr. Kagame's forces had carried out a highly targeted campaign against Rwandan and native Congolese Hutu, some of whom had fled to Congo after the genocide. Some experts have put the death toll as high as 300,000 people. The overwhelming majority of these victims, according to the report, were unarmed, including large numbers of women, children and the elderly. (The Rwandan government called the U.N. report "outrageous" and "amateurish.")

As a foreign correspondent at the time, I followed these people as they crossed the enormous breadth of Congo by foot, their numbers dwindling as they came under attack by Rwandan forces and fell from disease. But the U.S. ambassador to Congo at the time, Daniel Howard Simpson, said that humanitarian concern about these refugees was misplaced. "They are the bad guys," he told me in 1997, justifying Washington's silence. Years later, the U.N.'s investigation reached a different conclusion: "The apparent systematic and widespread attacks described in this report reveal a number of inculpatory elements that, if proven before a competent court, could be characterized as crimes of genocide."

Filip Reyntjens, a Belgian scholar and leading expert on Rwanda, wrote last year that Mr. Kagame, for all his "vision and ambition," was "probably the worst war criminal in office today." But 20 years after the genocide, Mr. Kagame—tall, gaunt and severe-looking—tours U.S. college campuses, where he receives honorary degrees and is toasted by the great and the good of the Western world.

Western sympathy and guilt over the genocide explain much of this, but Mr. Kagame also has excelled at conveying an image of Rwanda as something new to Africa: a capable, technocratic state dedicated to good governance, a regional financial hub and an Internet-for-all society. "They are extremely adept in speaking a discourse that Westerners want to hear," said Catharine Newbury, a Rwanda specialist at Smith College.

Rwanda remains extremely poor, but it has recently sustained fast growth rates, and health care, longevity, education and gender equality have improved strongly. Still, Mr. Kagame is best seen not as a modernizing technocrat but as an unapologetic autocrat. He bullies his neighbors, rewards his cronies and menaces dissidents.

The U.S. State Department says that it is troubled by what appear to be the politically motivated killings of a number of high-profile Rwandan exiles. When Rwanda's former spy chief was found dead in a Johannesburg hotel in January, Mr. Kagame denied any involvement but added, in an interview with The Wall Street Journal, "I actually wish Rwanda did it. I really wish it."

The country's ruling party, the Rwandan Patriotic Front, also controls a vast array of business interests in Rwanda, experts say—managed totally off-budget. "Kagame is the only one who knows how much money this is or how it is spent," said Theogene Rudawingwa, a dissident in exile who was once Mr. Kagame's chief of staff.

Recently, U.S. diplomats have taken Mr. Kagame to task for supporting militias in Congo. But critics say that Washington must go much further to improve the course of post-genocide Rwanda. With Mr. Kagame approaching the end of his constitutional term limits in 2017, a big opportunity looms. "There has to be an uncompromising position on opening up political space in the country and ending the destabilization of the Congo," saidScott Straus, a University of Wisconsin political scientist. "I don't think it will be easy, but more of the same isn't going to work."

Mr. French is a professor at Columbia Journalism School, a former New York Times foreign correspondent and the author of "China's Second Continent: How a Million Migrants Are Building a New Empire in Africa," to be published by Knopf in May.