BROWNSVILLE — Fernando Luna, the older brother of indicted Border Patrol agent Joel Luna, copped a plea last week. Now prosecutors are compiling a growing dossier on their baby brother Eduardo, identified as an alleged former member of the powerful Gulf Cartel.

All three brothers were indicted on capital murder and organized crime charges stemming from the beheading death of undocumented Honduran immigrant Jose Francisco “Franky” Palacios Paz in South Texas last year. The case has shined a bright light on homegrown cartel violence and alleged Border Patrol corruption on the U.S. side of the border.

New disclosures point to the central role allegedly played by Eduardo, 25, described in court papers and public statements as a Gulf Cartel “commander” with a history of violence — someone “very capable of killing anyone for no reason,” one former acquaintance claimed in a court affidavit made public last week. Both Eduardo and Border Patrol Agent Joel Luna, 31, a decorated Iraq war veteran, have pleaded not guilty to all charges.

Eduardo’s attorney, Gabriela Garcia, did not return phone and email messages Monday.

During a hearing last week, Joel’s attorney, Carlos A. Garcia, fought for a separate trial for his client on the grounds that he would be harmed by allegations about his younger brother’s violent past.

Garcia referred to statements made to investigators by a high-ranking Gulf Cartel ex-commander now locked up in Houston. The former capo, Juan Francisco Saenz-Tamez, nicknamed “Commander Pussy,” gave prosecutors damaging statements against Eduardo in a recent jailhouse interview, it was disclosed in recent court hearings. Saenz-Tamez, said in court documents to have served alongside Eduardo as a cartel “comandante,” is serving a 30-year sentence in a federal prison in Houston after pleading guilty to laundering $100 million while moving a half-ton of cocaine and 90 tons of marijuana through the United States.

“There are accusations of murders, accusations of kidnappings, extortions, quite troubling bad acts that I would anticipate the government will introduce in this case,” Garcia said in a Cameron County courtroom last week. “That bad information would then bleed over and somehow impugn my client and his lack of criminal history.”

Garcia’s argument all along has been that prosecutors are using a guilt-by-association strategy against his client Joel — basically tying the Border Patrol agent to the illegal acts of his siblings. Prosecutors, though, have said all three brothers were engaged in an organized “criminal enterprise” as a sort of family business. They point to the cocaine, cash, weapons — and even the agent’s commemorative Border Patrol badge and work station password — that authorities recovered from a safe that Joel allegedly bought and used.

Last week, State District Judge Benjamin Euresti ruled against Garcia’s motion for separate proceedings, signaling all three brothers would have to stand trial together. But an hour or so after his ruling, Fernando Luna, 35, the eldest of the three, made an unscheduled appearance before Euresti and took a plea deal. Fernando pleaded guilty to cocaine possession, and the state agreed to dismiss the far more serious murder and criminal conspiracy charges.

Under the terms of the deal, he will serve no more than three years and possibly get probation only, depending on how much he helps prosecutors in the sweeping murder and corruption probe.

The agreement has the potential to shake up the investigation. Another defendant in the case put both Fernando and Eduardo Luna at the crime scene — the Veteran’s Tire Shop in Edinburg, Texas — on the day of the March 2015 murder. Under the plea agreement, Fernando must “truthfully testify in this case and any other arising out of this investigation.” His defense attorney, Nat Perez, said the older brother could “very easily” end up testifying against his siblings in their trials.

Joel Luna’s attorney expressed confidence that his client would be exonerated, noting that the agent was at his Border Patrol station in another county at the time prosecutors believe Franky Palacios was killed. In the court papers filed last week Fernando’s wife, a Mexican citizen who has since been deported, is said to have told investigators Joel did not have any dealings with the Veteran’s Tire Shop.

“I feel confident — it’s based on what I know of the case — that my client didn’t have anything do with this murder, nor with any of the acts that led to the murder,” Garcia said. “The facts do not support any sort of finding that Joel had anything to do with what his brothers were up to.”

Five defendants in total were charged in the case. Two men not related to the Luna brothers, and who worked at the tire shop, have also pleaded not guilty and are to be tried separately. Officials say the defendants wanted to silence Palacios to keep him from snitching on their illicit activities. While drug trafficking was a focus of the original charges, lead Cameron County prosecutor Gus Garza suggested in court last week that there are more indications that gun running played a role in the alleged criminal enterprise.

Guns originating from Texas represented more than 40 percent of the U.S. weapons seized at Mexican crime scenes from 2009 to 2014 — far more than any other state, according to a recent report from the U.S. Government Accountability Office.

“The evidence now has shown the trafficking of weapons,” the prosecutor told the judge.

In July, The Texas Tribune reported on court affidavits highlighting Eduardo Luna’s suspected role as a member of the Gulf Cartel, and the unproven allegation that he killed Texas-born narco Mario Peña — nicknamed “El Popo” — after being kidnapped during a violent cartel shake-up in 2013.

In new court filings, prosecutors reveal more detail about Eduardo’s alleged activities inside the Gulf Cartel, which controls a large swath of territory along Mexico’s border with South Texas.

The filings show Peña’s sister told investigators of the time she met the youngest brother in Camargo, across the border from Rio Grande City, Texas, when her brother declared: “This is Commander Pajaro … He’s very young.” That nickname was engraved on a pistol found in the safe along with Joel Luna’s badge and work-related documents, and investigators believe “Pajaro” was brother Eduardo’s nickname inside the Gulf Cartel.

Jessica Peña reached out to investigators after seeing Eduardo’s picture plastered across TV screens last summer when he was arrested and charged with the murder of Franky Palacios; she told investigators he “had killed several more people before her brother,” the filings say.

Investigators wrote in their affidavits that Peña said Eduardo ” is a very dangerous person, and very capable of killing anyone for no reason. Ms. Peña advised after the interview that she is willing to fully cooperate with authorities in this case.”

Read more of the Tribune’s related coverage:

• When Franky Palacios Paz was found naked and decapitated floating off South Padre Island, the local sheriff thought the murder would lead investigators back to Mexican drug cartel violence. He didn’t expect a U.S. Border Patrol agent to be among those arrested.
• Rudy Soliz did it for sex. Sergio Lopez Hernandez blamed depression and financial trouble. The crimes differ, but prosecutors say the actions they’re accused of weakened the U.S. borders and ports of entry they were tasked with protecting.
• Whether most — or even a significant fraction of — corrupt federal border agents are caught and punished is an open question. Customs and Border Protection boasts of more stringent screening and monitoring of its agents but releases little data to back up its claims.

This story is part of The Texas Tribune’s yearlong Bordering on Insecurity project.