During the investigation, many witnesses, informants and Mexican law enforcement officials working with the task force were intimidated, tortured or killed, including Jose Patino Moreno, a crusading Mexican federal prosecutor whose head was crushed by an industrial press in 2000.
Over the years, several cartel suspects were captured and extradited, but the brothers remained out of reach. Benjamin was arrested and jailed in Mexico in 2002. Ramon was gunned down in Mazatlan the same year. Another brother, Eduardo, went into hiding.
When Javier Arellano Felix was intercepted in 2006 on his sportfishing boat, which was being tracked by the DEA through a global positioning system device, Duffy boarded the helicopter in San Diego. Soon after being lowered 150 feet from the helicopter, she was on the Coast Guard cutter, sitting across the table from the trafficker. He was wearing a tank top and flip-flops. Duffy offered him a soft drink and introduced herself.
"That kind of shows the grittiness of Laura Duffy, literally dropping herself from a helicopter," said Bartick, the defense attorney. "She took advantage of an opportunity to talk to him before he received legal representation."
Arellano Felix is one of seven cartel associates who have been sentenced in recent years. His brothers Benjamin and Eduardo are jailed in Mexico and are being sought for extradition.
In Tijuana, meanwhile, the organization's leadership has passed to a nephew of the brothers, Fernando Sanchez Arellano, who has found himself in Duffy's cross- hairs. The indictment she announced in July targeted dozens of his crew members. It's not clear if Sanchez Arellano himself has been indicted. Duffy wouldn't comment on his status.
Some authorities believe the young man has fled Tijuana. Others think he is flourishing as he revives his uncles' legacy. For some, the Tijuana cartel will survive so long as the Arellano name lives on.
Duffy appears to be trying to erase it.
In the indictment against the nephew's gang, it is referred to as the Fernando Sanchez Organization. Conspicuously absent is the infamous name: Arellano.
"The [Arellano Felix cartel] as we've known it no longer does exist," Duffy said.