Federal agents have exposed a shocking tale of illicit relationships between a worker at a government-sponsored shelter and an illegal immigrant boy she was supposed to be taking care of — and a plot by three employees to orchestrate a jailbreak, freeing him from custody.

The teen was an Unaccompanied Alien Child, the most vulnerable of migrants who arrive at the southwest border, coming without parents. UACs are supposed to get the highest levels of protection, with immediate transfer to social workers at shelters run under grants from the federal Health Department.

It was at one of those facilities — Southwest Key’s Casa Padre in Brownsville, Texas — that the teen, identified as Jeffry Nai Gonzalez-Melendez, was staying when the three women plotted to break him out, according to court documents.

Kevin J. Morehouse, special agent for U.S. Immigration and Customs Enforcement, said in a court affidavit that the agency discovered the plot this year when a contraband phone found in the possession of a child at the facility had nude photos of one of the staffers.

When agents questioned employee Evericka Velasquez, she let them see her phone. They discovered a chat with Karla Izaguirre in which the women plotted the boy’s escape.

Ms. Izaguirre, confronted with the evidence, admitted to the whole thing, according to the affidavit.

The three women arranged to have Mr. Gonzalez run away while he and other UACs were on a field trip away from the facility at the Harlingen Arts and Heritage Museum, the court documents charge. One of the women picked him up and delivered him to a bus station in town, where Ms. Izaguirre met him and began to harbor him.

“Izaguirre stated that she did help plan the escape of Gonzalez even though she knew he was illegally present in the United States. Izaguirre then states that for approximately three months she provided Gonzalez with food, clothing and shelter in her own home,” Mr. Morehouse told the court.

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Jessica Vaughan, policy studies director at the Center for Immigration Studies, called the case “a little shocking but not at all surprising.”

“When we have policies that encourage minors to come here illegally, and when the system is overwhelmed by the number of new arrivals, and when there are inflexible rules that assume every minor is an innocent young child when really most are older teenage boys, things are going to go wrong,” she said.

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The prosecution is a black eye for the UAC program, which has faced other allegations of sexual abuse of minors in federal custody.

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The agent didn’t say how Mr. Gonzalez was apprehended but did ask a judge to keep him in the country to serve as a witness against Ms. Izaguirre.