Mexico City: Hiding out in a gritty slum, a politically connected couple believed to have ordered an attack that killed six people and left 43 students missing in September tried to lie low as dozens of federal agents staked out their suspected hiding spots.

Federal police seized Jose Luis Abarca and his wife, Maria de Los Angeles Pineda, in a raid before dawn in Iztapalapa, a working-class neighbourhood of the capital. It was a steep fall from their reign of wealth and power as the mayor and first lady of Iguala, a town in southern Guerrero state where the students from a teachers’ college went missing September 26, allegedly at the hands of police and a drug cartel.

Attorney-General Jesus Murillo Karam said on Tuesday that 60 federal agents had spent about a month staking out three houses in the neighbourhood. He said they were tipped off to the couple’s presence by trailing a female associate, Noemi Berumen, who apparently accompanied the couple or aided them in their flight from justice. Berumen was also detained in the raids.

“The house they were found in looked as if it were abandoned,” Murillo Karam said. “The reason we started to suspect this person [Berumen] ... was that she appeared to be entering an abandoned house.”

The capture did nothing to answer the biggest mystery: Where are the 43 students who haven’t been seen being taken away by officers after the deadly attack by police in Iguala on September 26. Their disappearance, and the failure to make progress in the case, has ignited protests across the country and broadsided President Enrique Pena Nieto’s efforts to paint violence in Mexico as a thing of the past.

“News like this just makes you angrier,” said Mario Cesar Gonzalez, whose son, Cesar Manuel Gonzalez, is among the missing students. “I wish they would put the same intelligence services and effort into finding the students. The ineptitude is staggering.”

Authorities have uncovered clandestine mass graves and the remains of 38 people during the search for the students, but none has been identified as the missing youths. Besides Tuesday’s arrests, at least 56 other people have been taken into custody, and the Iguala police chief is also being sought.

Some hoped the couple’s detention would provide new leads.

“This was the missing piece. This arrest will help us find our kids,” Felipe de la Cruz, the father of one of the missing students, told Milenio television. “It was the government who took our kids.”

Before they fled last month, the couple ran Iguala like a fiefdom in cooperation with the local drug cartel, Guerreros Unidos. Abarca received up to $220,000 (Dh808,080) every few weeks as bribe money and to pay off his corrupt police force, according to Murillo Karam, who gave a detailed account last month of the couple’s alleged collusion with organised crime.

They had built a fortune from real estate holdings, including jewellery stores and a shopping mall that was hit by vandals protesting the students’ disappearance. They allegedly used their ties with a local drug gang to amass those riches, and prosecutors say they used the same drug gunmen to get rid of perceived enemies, including the students from a radical teachers college.

The mayor’s wife was a major operator in the cartel, an offshoot of the Beltran Leyva gang, Murillo Karam said. Two of her brothers were on former President Felipe Calderon’s most-wanted drug trafficker list until they were killed in 2009. A third brother, Salomon Pineda, was believed to run the territory in northern Guerrero state for the cartel.

Guerreros Unidos has increasingly turned to the lucrative practice of growing opium poppies and sending opium paste to be refined for heroin destined for the U.S. market, according to a federal official.

The missing students attended a radical rural teachers college with a history of carrying out protests. They had gained the enmity of Abarca because of a previous demonstration in Iguala, Murillo Karam said. Abarca believed they planned to disrupt a speech by his wife, who aspired to succeed him as mayor, and he ordered police to detain the students after they hijacked four buses to provide transportation to a coming protest.

Three students were shot dead in the confrontation and later three bystanders were killed in a separate attack.

Police picked up the other 43 students and took them to the nearby town of Cocula, Murillo Karam said. At some point they were loaded aboard a dump truck and taken, apparently still alive, to an area on the outskirts of Iguala where some mass graves have been found, he said.

Detained gang leader Sidronio Casarrubias told authorities one of his lieutenants told him the students were sympathisers of a rival gang, the attorney general said.

In statements to the media soon after the disappearance, Abarca maintained he spent the evening of Sept. 26 dining out and said he ordered police to leave the students alone.

The search for the students has taken authorities to the hills above Iguala and to a gully near a trash dump in the neighbouring city of Cocula, but still no remains have been identified.