But Mr. Valdez’s work and international profile, they figured, protected him. He was known and beloved by local and foreign journalists alike, and was the recipient of awards and recognition globally.

His death and the subsequent targeting of newsroom leaders exposed two of the most devastating risks to the freedom of expression in Mexico today.

One is the physical threats to journalists and, by extension, freedom of speech in Mexico. More than 47 journalists have been killed since Mr. Peña Nieto took office in late 2012, 15 of them after Mr. Valdez’s death in May of last year, according to Article 19, a journalist protection group.

“We believed that a journalist as prestigious as Javier was untouchable,” Mr. Bojórquez said.

“When they killed Javier, we understood from that point on that they could kill anyone,” he added. “We understood that the paradigm had been broken.”

The second risk is a separate but connected facet of the rule of law in Mexico: There is essentially near total impunity when it comes to how it is broken or applied — a dynamic underscored by the use of illegal spyware to intimidate and spy on pro-democracy voices.

Dating back to 2016, the target list has been a who’s who of Mexico’s most prominent voices aiming to bring accountability to the nation, including the directors at Rio Doce.

Mr. Bojórquez said he and others had become aware of the government’s potent spyware in February 2017, when the Citizen Lab and The New York Times published articles outlining its illicit use against backers of a nationwide soda tax.