The 58-year-old, who was arrested Friday while on the run, is accused of organized crime and kidnapping, according to the Associated Press. Officials believe he followed orders from the former mayor of Iguala to get rid of the students, most of whom were young men, and then tried to cover up Iguala police's role in the disappearance.
“The investigations indicate that this person was one of the people responsible for coordinating the operation that turned into the aggression against the students,” Renato Sales, head of the National Security Commission, said in a news conference on Friday.
Attorney General Arely Gomez tweeted that Flores's arrest “will allow the collection of key testimony to clarify the facts of Iguala,” according to the AP.
Authorities have arrested 131 people, including Iguala's former mayor, Jose Luis Abarca, and his wife, Maria de los Angeles Pineda, in connection with the mass disappearance. Prosecutors accuse Abarca and his wife of masterminding the alleged kidnapping. The two were arrested in 2014.
Seventy of those arrested are police officers and alleged cartel members. Many of them have claimed they were tortured by officials, the AP reported.
The students from a teaching college in Ayotzinapa, more than 150 miles away from Iguala, were last seen alive Sept. 26, 2014, when they were crammed into police cars. They traveled to Iguala that day to protest education reforms. At some point they hijacked a bus and were stopped by police officers who opened fire at them. They have not been seen or heard from since.
An earlier theory on the students' disappearance was that Iguala police handed them over to drug cartel assassins, who shot them and burned their bodies outside the nearby town of Cocula, The Washington Post's Joshua Partlow reported last year.
But independent investigators who've reviewed evidence in the case have disputed the theory that the students bodies were burned and claimed that Mexican authorities tortured witnesses and mishandled evidence.
The outside experts, convened by the Inter-American Commission on Human Rights, prepared a 400-page report questioning claims by Mexican authorities on how the crime unfolded, Partlow wrote. Their investigation, which included interviews with prisoners, witnesses and government officials, found that victims' clothes found by authorities had not been examined and surveillance videos were erased.
The report, which came out nearly a year after the students vanished, also point to signs that the buses the students stole were used to transport heroin into the United States, and they may have inadvertently hijacked buses that contained drugs.
The students' disappearance prompted violent riots in towns including Ayotzinapa, located in the troubled rural state of Guerrero in southern Mexico.
“The parents are enraged by so much waiting and so few results,” Felipe de la Cruz, whose son, Angel, is one of the missing students, told a crowd during a protest in November 2014, Partlow reported. “The flame of insurgency has been lit.”
De la Cruz, who has emerged as a spokesman for the victims' families, said Friday that he hopes the arrest of the former police chief “leads to some good news for us.”
“We hope that what he says takes us definitively toward the truth and to where the youths are, because that's what we've looked for all this time,” he said, according to AP.
The lack of closure on the students' disappearance has so far become an embarrassment to the administration of President Enrique Peña Nieto.
Last Sept. 26, on the second-year anniversary of the students' disappearance, thousands of protesters took to the streets in Mexico City, the Los Angeles Times reported.
“I can't believe that we are here, two years later, with the same pain, the same demands,” protester Patricia Beltran, a 25-year-old student, said. “The government laughs at people's pain, but we are here today to tell them that it is not only the parents of the 43, but all of Mexico that insists that this government do its job.”