[W]hen I raised the subject with a former D.E.A. agent who has spoken to Mexican counterparts involved in the operation, he had a different explanation. “The marines tortured these guys,” he told me, matter-of-factly. “They would never have given it up, if not for that.” The D.E.A. refused to comment on the torture allegation. However, two senior U.S. law-enforcement officials told me that, though they had no specific knowledge of the Mexican authorities using torture in the operation, they “wouldn’t be surprised.”

Mexican officials deny it.

Eduardo Sánchez, the spokesman for the Mexican government, denied the allegation, and maintained that, in this and other operations, “federal officials, agents, and officers perform their duties strictly within the applicable legal framework and with utmost respect for human rights.”

Keefe cites a 2011 Human Rights Report:

A 2011 Human Rights Watch report found that members of Mexico’s security services “systematically use torture to obtain forced confessions and information about criminal groups,” and documented the use of such techniques as “beatings, asphyxiation with plastic bags, water boarding, electric shocks, sexual torture, and death threats.” The broad employment of brutal techniques, coupled with the high profile and the urgency of the hunt for Guzmán, makes it seem all the more plausible that Mexican authorities used unsavory, and illegal, means to pursue him.

Keefe also says the DEA were in Mazatlan the night before the capture (not just the joint base of operations in Baja.)

On the night of Friday, February 21st, about forty marines assembled in the city, along with a small contingent of agents from the D.E.A., the U.S. Marshals, and the Department of Homeland Security. The marshals, who specialize in locating fugitives, had been able to trace the signal on Condor’s BlackBerry to the Hotel Miramar.

He also says the DEA's Special Operations Unit have been monitoring his phones and emails since 2012:

By early 2012, the D.E.A. had homed in on Guzmán’s BlackBerry, and could not only monitor his communications but also use geolocation technology to triangulate his signal.

...The D.E.A. agents who monitored his e-mails and texts marvelled at the extent to which his communications seemed focused not on managing his multinational empire but on juggling the competing demands of his wife, his ex-wives (with whom he remained cordial), his girlfriends, and his paid consorts. “It was like ‘Peyton Place,’ ” a former law-enforcement official who kept track of the communications told me. “It was a non-stop deal.”

El Chapo caught on to what they were doing and set up an elaborate system to avoid it. To no avail, according to O'Keefe:

Nevertheless, by studying the communications patterns of the cartel, analysts at the Special Operations Division of the D.E.A. eventually grasped the nature of the arrangement. They resolved to focus on the small ring of logistical facilitators surrounding Guzmán, to identify the mirrors that he was using, and, ultimately, to target their communications.

The electronic and phone interceptions ramped up after the capture of "El Chino" Antrax in Amsterdam (he's awaiting extradition to San Diego):

At the D.E.A., which taps hundreds of phone lines and e-mail accounts associated with traffickers, the process of applying pressure to a criminal organization and then monitoring furtive attempts at outreach is known as “tickling the wires.” ....

As the cartel attempted to regroup, authorities on both sides of the border intercepted scores of phone calls, texts, and e-mails. They learned that Guzmán would soon be coming to Culiacán, the state capital of Sinaloa, for a meeting with his sons Alfredo and Iván—ascendant traffickers who were both close friends of El Chino Ántrax.

The DEA gave the information to the Mexican Marines, and Operation Gargoyle (to catch Chapo) proceeded. They set up operations near Los Cabos in the Baja peninsula, and were soon joined by U.S. agents.

Keefe says President Pena-Nieto knew about the operation and gave the Marines 3 weeks to catch Chapo -- after that he wanted to proceed with plans to go after the Knights of Templar. He says a spokesman for the Mexican Government denies this.

Keep in mind Keefe's sources are mostly U.S. law-enforcement, who may be trying to spin events. Some of the "former" agents claim to have spoken to agents involved in the take-down, but who knows if they are telling the truth or if they are accurately repeating what they heard. There are a lot of versions of the capture and many differ in the details.

Gerardo Reyes of Univision wrote a lot of this special series about El Chapo. The chapter on the capture, in English, is here. Reyes, like Keefe in his excellent 2012 New York Times Magazine article, Cocaine Incorporated, ordered court transcripts for background and historical information. Obviously, there are no such transcripts yet pertaining to El Capo's capture, but I still hesitate to put too much stock in current accounts from anonymous and retired law enforcement sources.

Another reporter, Luis Chaparro of El Diario has been writing about an informant (who formerly worked at an ER in Juarez where the Sinaloa cartel would bring the wounded) who says he is the one who tipped the DEA off to El Chapo's phone by getting the number for the phone of Emma Coronel, his wife, from her cousin. He went to work as an informant for the DEA around August, 2013, and set up the arrest of Mario Nuñez Meza, alias "El Mayito" or "M-10. Then in January, he gave them the information on Emma's phone, which he says is the phone that led to El Chapo's capture. He says the U.S. has stiffed him, and instead of paying him the reward, it is deporting his wife and has terminated his immigration permit that allowed him to be "paroled" into the U.S. He has now filed for asylum. Chaparro says he has confirmed the man's informant status and help with El Chapo's capture with the DEA and viewed documents supplied by the informant's lawyer.

There is a lot that still is not clear about Operation Gargoyle, particularly the nature and extent of the interception of phones and electronic communications, and the degree of involvement U.S. involvement in the capture.

It does appear, though, that Mexico is not happy with the U.S. "snitch and release" policy, particularly as to Jesus Vicente Zambada-Niebla, and as a result, we won't be trying Chapo anytime soon in the U.S. Mexico is not going to chance Chapo's airing dirty laundry about Mexican officials in exchange for a shorter sentence.

A hearing is set for this morning in the Illinois case of Alfredo Vasquez-Hernandez, co-defendant of El Chapo and Zambada-Niebla. I won't be surprised if he has decided to plead guilty after all, now that it's been made clear he hasn't cooperated. His trial is set for May, and other than the issuance of a few subpoenas to incarcerated individuals (sealed), there's been no action for weeks -- no recent Government trial memorandum, no proposed jury instructions or voir dire. If he pleads, we may never get to hear the Flores twins sing.