When her parents denied her food and water for eight days, the girl said that she knew she was going to die, just like her two younger siblings. For days, her parents had beaten her when they caught her sipping water or looking for food. Famished and frail, she said they dressed her in special attire worn for death.

“The children were not supposed to eat, so they could die,” the child, a 9-year-old identified only as EG and hidden inside a witness protection booth, told a packed courtroom on Thursday in the coastal Kenyan city of Mombasa.

She was among the first witnesses to testify last week in the manslaughter trial of Paul Nthenge Mackenzie, an evangelical pastor accused of commanding members of his church to starve their children and themselves to death in order to meet Jesus in the end times.

The pastor and 93 other defendants, including his top associates and some of his followers, denied the manslaughter allegations and pleaded not guilty at the start of the trial.

Since April last year, 429 bodies have been exhumed from shallow graves in the Shakahola Forest in southeastern Kenya, where members of the doomsday cult lived, the authorities said. While some died of starvation, others were strangled, beaten and suffocated, according to the lead government pathologist. Dozens of people have been rescued, but hundreds more are still missing, officials say.

For the last 16 months, the East African nation has been both riveted and horrified by the story of how one man was able to convince hundreds of people that the world was coming to an end and that they should follow him into a forest teeming with wild animals.

At the Mombasa Law Courts last week, the suspects arrived chained in pairs — except for Mr. Mackenzie and his second-in-command, Smart Mwakalama, who each walked in alone and in handcuffs. In the humid, packed courtroom, the defendants sat looking forlorn, with some drifting to sleep as the proceedings got underway. None of the victims’ family members were there; many of them are day laborers lacking the time or money to attend hearings regularly, activists said.

A few of the suspects appeared weak; during a lunch break, a prison guard was heard voicing her concern to another officer about one defendant’s reluctance to consume the bread and milk she had been given.

One suspect died in jail, the authorities said last week, and an inquest was underway to determine the circumstances of that death.

As witnesses arrived, security officers, some carrying guns, stood shoulder-to-shoulder to prevent the suspects from seeing them. Prosecutors said they had lined up 90 witnesses, including minors, to take the stand in the case. Among them are 13 anonymous witnesses, referred to only by their initials, and whose voices were beamed from a speaker atop the enclosed witness booth.

The gathering in the forest grew during the Covid-19 pandemic, with the expanding congregation building makeshift homes in areas given biblical names like Bethlehem and Jerusalem. There, witnesses said, at Mr. Mackenzie’s urging they began plans to starve the children first before the adults could join them.

As they deprived the children of food, parents would make them wear special clothing, they said.

“Those are my death clothes,” the 9-year-old told the still courtroom after she was shown an exhibit submitted as evidence inside the enclosed booth. The clothes were not shown to spectators in the courtroom.

She said she was wearing those clothes when officers rescued her. By then, her two younger siblings, whom she had tried to save by giving them water, had starved to death before her eyes.

The witnesses faced intense cross-examination from the defense lawyer, Lawrence Obonyo, who questioned their memory of events and where and when they heard Mr. Mackenzie say they should starve. Another witness, a 17-year-old girl identified as JCK, gave conflicting accounts about where they lived after her mother pulled her from school.

Activists and human rights groups have criticized the length of time prosecutors took in starting the trial, saying it could hamper the victims’ ability to deliver crucial testimony. Hearings in the trial will resume on Sept. 9.

They have also questioned the government’s choice of defendants. Some of those being tried “are victims themselves and should not have been charged,” said Shipeta Mathias, a rapid response officer with HAKI Africa, a Mombasa-based human rights organization. Mr. Mathias was among the emergency workers who arrived at Shakahola last year when some of the rescued church members were still refusing to eat.

“We had to lie to some of them that we had been sent by Jesus so they could eat,” he said of some of the defendants. “They are brainwashed, and they need help.”

The case has also shined an uncomfortable spotlight on the effectiveness of Kenya’s police force.

Families searching for their loved ones say they sought help from law enforcement, but in vain. Local community members, suspicious about the activities in the forest, filed numerous reports with the police, who failed to follow up or investigate. Rights groups also criticized the force for not monitoring Mr. Mackenzie, who was arrested several times and, at one point, even charged with radicalization and promoting extreme beliefs, though that case went nowhere.

Family members and their advocates say they are also frustrated with the slow rollout of DNA testing. Just three dozen bodies have so far been matched with family members, officials and activists say, disappointing those who want to give their loved ones the final dignity of a proper burial.

“What we need to get is justice for the people we lost,” said Paul Chengo, a manual laborer who said he was missing six members of his family. “What we need is closure.”

Mohamed Ahmed contributed reporting from Mombasa.