Before being taken to the killing ground where he now works as a tour guide, Emmanuel Murangira sought refuge at church. It was April 1994, and as Hutu extremists swept through the countryside hunting Rwanda's Tutsi minority, millions were clamoring for refuge in the Roman Catholic churches that sit atop the country's lush green hills like crowns.

Murangira joined the thousands at the elegant compound of Bishop Augustin Misago, head of the Gikongoro diocese about 100 miles southwest of Kigali, the Rwandan capital. But Misago told the terrified arrivals they must move on, sending them to the nearby classrooms of a technical college that today is a memorial filled with the smell of formaldehyde and the mummified corpses of 2,700 children, women and men.

That is a fraction of the thousands slaughtered there on the night of April 19, 1994.

"We went to Misago's place, and they brought us here," said Murangira, a gaunt figure with a perfectly round depression above his left eye, the entrance wound of the bullet that punctured his brain. "He was with the government and supported the killing of all these people here."

From the dock of the tribunal where he stands as the first Catholic bishop charged with genocide, in the most Catholic nation in Africa, Misago, 56, denies it all.

He will be tried in a Rwandan court -- the First Instance Tribunal of Kigali -- that routinely sentences "category one" genocide defendants to death. He will not be tried by the United Nations war crimes tribunal for Rwanda, where the ultimate penalty is life imprisonment.

The difference, according to the defendant, is crucial. Dignified even in the pink summerweight pajamas of a Rwandan prison inmate, Misago insists he is but a convenient scapegoat for the reservoir of bitterness Rwanda's post-genocide government harbors against the Catholic Church.

That government was formed from the Tutsi-led rebel army that stopped the slaughter of more than 500,000 Tutsis and moderate Hutus, most of whom met their deaths in and around holy places. Twice before in Rwandan history, in 1959 and 1963, Catholic churches had provided sanctuary against ethnic violence. The fatal difference in 1994, Rwandan officials say, was the close ties between the church's top officials in Rwanda and the forces bent on genocide.

"This is Misago," said prosecutor Edouard Kayihura as proceedings opened earlier this month. "If it happens that the church is also tried, so be it."

The case has alarmed the Vatican, which called Misago's arrest "an extremely serious act which hurt not only the church in Rwanda, but the entire Catholic Church." So far, the Vatican has stuck by Misago, paying for his lawyers and offering moral support. At the same time, the trial underscores the contrast between the actions of church leaders in Rome and those inside a country where people were being chopped, shot and burned to death at the rate of 5,000 per day.

The Vatican condemned the Rwandan genocide only days after it began. By contrast, Rwanda's archbishop offered only tepid statements, maintaining an ambiguous stance right up to the moment rebel soldiers killed him and three other bishops.

The silence was especially egregious given the church's special authority in Rwanda. With a church membership of 62 percent of the population before the genocide began, the national culture includes a tradition of obedience to authority that Hutu extremists exploited in mobilizing the majority population against the Tutsi minority.

"The church is a very strong institution," said Jean de Dieu Mucyo, the Rwandan justice minister. "It's like a government on its own. If they had gone around preaching and saying, `Stop the genocide,' a lot of people would have been saved."

Hundreds of clergy were slaughtered, many after refusing to turn refugees over to the Hutu militias that carried out most of the killing. Others are notorious, including Father Wenceslas Munyeshyaka, a Hutu who mounted the pulpit at Sainte Famille Catholic Church in Kigali wearing a flak jacket and side arm, and allegedly selected mistresses from among the Tutsis who sought sanctuary. He awaits trial in France, where he fled.

But Misago, a Hutu, is the highest church official accused of helping organize the genocide. He acknowledges the activity at the heart of the prosecution's case -- that he attended meetings with local and district officials who carried out orders from the capital to exterminate the Tutsis. The bishop insists, however, that he was present only to try to protect those in danger.

"I'm innocent," he said.

His trial has proceeded fitfully, with week-long recesses at the bishop's request. The first phase involves questions from a panel of judges -- witnesses will be called later -- and Misago's answers have been rambling and sometimes contradictory. At one point last week, Misago testified, "In all the meetings I attended, they never discussed anything like killing or anything." Later in the same day he claimed, "It was very important for the church to attend these meetings, to convince them to try to reduce the killing, or to stop it altogether."

The bishop had only an angry reply to a letter one judge read aloud, in which Tutsi students who survived the genocide described how Misago separated them from Hutu students. "All these kids, they go around lying," Misago retorted. "They don't know anything."

In the crowded gallery behind him, genocide survivors chuckled and tisked.

Aloys Habimana, who has monitored scores of genocide trials for the independent Rwandan League for the Promotion and Defense of Human Rights, said that despite appearances, the government faces an uphill battle.

"To prove planning genocide is not easy against someone who was not in the government," Habimana said. "They want to show the bishop was close to the government, but something is missing."

He said the prosecution case sometimes appears ill-prepared, an observation that underscores the political aspect of the trial. Misago was arrested just a week after being singled out by President Pasteur Bizimungu in a speech marking the fifth anniversary of the genocide.

A Western diplomat said the case is being watched closely for fairness. "We have several times told the Rwandan government, `This is the test,' " the diplomat said. " `The international community will judge you on this trial.' "

Alison Des Forges of New York-based Human Rights Watch, who has followed events in Rwanda for decades, said "It's been clear for five years that the political use of justice is tolerated" by the present government.

Habimana said many observers were surprised to see a mere bishop arrested when the government has acknowledged investigating Thaddeo Nthinyurwa, the current archbishop. Nthinyurwa, who during the genocide served as bishop of Cyangugu, the diocese adjoining Misago's, said in an interview that his conscience is clear.