Moments before paramedics rushed Roxsana Hernandez out of an ICE jail in New Mexico, Charlotte consoled her dying friend.

“I wasn’t sure if I was going to see her again,” she said. “So I hugged her and told her, ‘God bless you. Take care. We’ll be here when you get back.’”

They’d known each other only a few months, but the Honduran women had formed a tight bond, traveling to the U.S.-Mexico border together last spring in a highly publicized migrant caravan and petitioning for asylum in San Ysidro (San Diego County). As openly transgender women, the pair were running from the grip of death in one of the most violent countries in the world.

But only one would survive the treacherous 2,700-mile journey. Only one would have a chance at a new life.

Hernandez died from cardiac arrest and complications from HIV in May, sparking outrage and renewing a debate on the treatment of transgender people in detention facilities. The mystery and controversy behind her death lingers — an independent autopsy revealed signs that Hernandez was abused and neglected while in the custody of the Immigration and Customs Enforcement agency, according to her family. The agency has contested the allegations.

Nine months later, Charlotte is piecing her life back together, hoping to start over in the Bay Area. But the trauma of her journey is unrelenting, often transporting her back to dark moments she desperately wants to forget.

“You think you’re fleeing a difficult situation only to find yourself in an even worse situation,” said Charlotte, who described in Spanish her treacherous journey through Mexico in an hour-long interview last month. “Being trans and traveling in a caravan is extremely difficult. You experience a lot of discrimination from the same people who are traveling alongside you, and sometimes from people in Mexico.”

Charlotte asked that The Chronicle identify her only by first name, because she fears consequences to her pending asylum case and retribution by gangs in Honduras, which threatened her life on several occasions. She’s part of a skyrocketing number of asylum seekers who have flocked to the U.S. in recent years, even as the Trump administration looks to turn them away.

Her story illustrates the plight of lesbian, gay, bisexual and transgender migrants in particular, who face extreme violence and discrimination in their home countries. There were 264 recorded deaths of LGBT people in Honduras from 2009 to July 2017, including 152 gay men and 86 transgender people, according to a report by Amnesty International.

The journey to the U.S. can prove just as deadly. Trans women are particularly subject to harassment and threats in Mexico from police and immigration agents, drug traffickers and other migrants, according to lawyers.

“They have suffered pretty severe and often extreme forms of physical and sexual violence, often from a very young age,” said Wes Brockway, an attorney with the Santa Fe Dreamers Project, which initially took on Charlotte’s case while she was detained in New Mexico. “It’s from family members, often it’s from classmates, but we’re seeing a lot more incidents from members of gangs, police officers and government officials themselves.”

Meanwhile, organizations in the Bay Area are expanding their efforts to connect LGBT asylum seekers with sponsors who can provide housing and other needs.

Advocates believe they have the best chance at winning cases in San Francisco, where there’s more awareness about the asylum process and understanding of transgender issues, said the Rev. Deborah Lee, executive director of the Interfaith Movement for Human Integrity in Oakland.

“Because the risks are so high — if they get deported it could mean a death sentence — it’s really important that they’re getting the best chance to win their case,” Lee said. “We want them to thrive, and land in a place where they’re going to have a fighting chance.”

Brockway, whose organization has represented nearly 40 transgender women in asylum cases during the past year, and about 75 on requests to be released from ICE detention on bond or parole, said LGBT migrants typically have a high probability of winning asylum because of their vulnerable circumstances.

“There’s extremely high rates of violence against LGBTQ individuals,” he said. “It’s very well documented. The women who are coming and are presenting their claims with legal counsel are often very successful.”

ICE, U.S. Customs and Border Protection and the Executive Office for Immigration Review said they don’t specifically track the number of LGBT asylum seekers who cross the border each year. There were 111 self-identified transgender individuals in custody at 20 ICE facilities nationwide as of Feb. 4, according to the agency.

Charlotte, who recently found a pro bono attorney in the Bay Area, checks in with ICE regularly and is awaiting a preliminary hearing in San Francisco Immigration Court this month.

Charlotte said MS-13 gang members in Honduras had pressured her to transport drugs into the factory where she worked in San Pedro Sula, an industrial city in northern Honduras. The drugs were popular among workers who used them to stay awake during long shifts, she said. But after Charlotte refused to be a mule, the gang began to send death threats.

“Why did they approach me, why did they choose me? Because in Honduras, identifying or looking trans means being the focus of jokes and criticism,” Charlotte said. “They don’t value our lives as human beings. This group uses this as an advantage for them and a disadvantage for us, because we’re forced to do things for them. … You can run away and move, but they send you death threats and tell you they’re going to kill you, like they did with me.

“I decided to leave my country and flee for my life because I wanted to keep living.”

Like many people who flee Central America by foot and travel north, Charlotte’s journey is defined by a complex labyrinth of unknown cities, long bus rides, shelters and a jumble of fractured memories.

She arrived in Mexico in 2016, settling in Tapachula, a city in the southeast state of Chiapas near the Guatemalan border where immigration authorities granted her asylum, she said. But when her grandfather died in Honduras that summer, Charlotte returned home to attend his funeral. It wasn’t long before MS-13 members tracked her down after the ceremony, raping her in a remote area in her hometown and threatening to kill her if she didn’t leave, she said.

“It was terrible for me because they forced me to do things that I didn’t want to do,” she said. “But I didn’t say anything to anyone because it was MS-13.”

Charlotte left for Mexico that night, returning to Tapachula for a few days before hopping on a bus to Mexico City, where she stayed at a shelter for about eight months. Then, she caught wind of a caravan approaching.

Migrant caravans from Central America, which often include more than 1,000 people, have become a growing phenomenon in recent years and a symbol of defiance against President Trump’s hard-line immigration policies. The caravans have particularly fueled Trump’s demands for a $5.7 billion border wall, elevated by claims that criminals and drug traffickers travel with the groups.

Charlotte went to Puebla and joined the caravan May 5. That’s where she met Roxsana Hernandez and about 30 other LGBT people.

“That’s where the travesty began,” she said.

The group faced taunts and threats throughout the journey, according to Charlotte. They were turned away at several churches and told they had to dress like men if they wanted food and other needs. At a shelter in Tijuana, neighbors yelled for the women to leave and threatened to run them over when they walked outside, she said. One night when Charlotte and her friends went out, a group of six men set the shelter on fire.

“All of our things burned. Our clothes, our makeup. Everything burned,” she said.

Charlotte — soft-spoken, guarded and funny — sat in the colorful offices of El/la Para TransLatinas, a nonprofit that provides health and educational resources to transgender Latinas in San Francisco. The women who run the group out of a rundown building on 16th street have become an adopted family to Charlotte, who takes BART from El Cerrito to visit. At the center of the office is a wall-to-wall altar honoring trans women who have died.

Charlotte held a small photo of Hernandez, smiling in a white lace blazer, her beach-blond hair pulled to one side. Though she was cropped out of the photo, Charlotte’s hand remains in the frame, resting on her friend’s shoulder.

The group crossed the border at the San Ysidro Port of Entry near San Diego on May 9. They spent several days in a holding cell — dubbed “la hielera” or “the cooler” for its extremely low temperatures — as they waited to be transferred to ICE detention. By then, Hernandez’s health was deteriorating, according to Charlotte.

The women were transferred to a unit for transgender inmates at the Cibola Correctional Facility in New Mexico on May 16, according to ICE records. Hernandez had stopped talking and eating. Her friends requested medical help.

Less than two weeks later, she was dead. Other individuals detained in the same unit as Hernandez who were quoted in the independent autopsy report allege that she showed symptoms of severe dehydration while in ICE custody but didn’t receive medical treatment until she was gravely ill.

She and Charlotte, who experienced severe stomach pain while in detention, had briefly seen a doctor in San Diego. But Hernandez, who had previous deportations and criminal charges for prostitution in the United States, was told she couldn’t be treated for HIV-related symptoms, according to Charlotte. There’s no record of the San Diego hospital visit in Hernandez’s official death report.

“Yes, she was sick throughout the journey, but she wasn’t dying. She could’ve lived longer,” Charlotte said. “They put a human being’s health as second priority. And that should never be the case. My friend lost her life because of that.”

Dr. Kris Sperry, the forensic pathologist who was hired by the Transgender Law Center to conduct the independent autopsy, has faced controversy in the past. Sperry stepped down in 2015 from his post as chief medical examiner for the state of Georgia after a news investigation revealed he had taken on hundreds of private cases while employed by the state.

ICE said it cannot speak to the validity of the private autopsy performed on Hernandez, but that allegations she was abused in ICE custody are false.

“A review of Hernandez’s death conducted by ICE Health Service Corps medical professionals confirmed that she suffered from a history of untreated HIV,” the agency said. “At no time did the medical personnel treating Ms. Hernandez at Cibola General Hospital or Lovelace Medical Center raise any issues of suspected physical abuse.”

Meanwhile, hundreds of miles away in Richmond, Debbie Bayer and her partner, David Reinertson, got a call from an advocacy organization asking if the couple would be willing to sponsor Hernandez and Charlotte once they were released from ICE detention. Bayer communicated with Charlotte often and filled her commissary account but had trouble reaching Hernandez.

“I kept calling, and everybody said, ‘We don’t know where she is,’” said Bayer, 69, a retired nurse. “She was already dead, I think.”

They welcomed Charlotte into their modest two-bedroom home in August.

“I had never housed a stranger before,” Bayer said. “I didn’t have any experience with trans people. When I went to the airport in Oakland I immediately thought, ‘She’s beautiful.’”

Charlotte is learning English and hangs out often with friends from the caravan and from El/la. She’s eagerly awaiting her work permit, which will allow her to get a job while her asylum case makes its way through the court. But on some days, her mind is with Hernandez.

“We were both supposed to come to this house,” she said. “That’s why I feel as if our story wasn’t finished yet. It was supposed to continue.

“But God knows why he does things.”

Tatiana Sanchez is a San Francisco Chronicle staff writer. Email: tatiana.sanchez@sfchronicle.com Twitter: @TatianaYSanchez