Pesquera said he found police cruisers with 300,000 miles on them, flat tires and dead batteries. He had to order 16,000 pairs of pants because cop uniforms were largely frayed. Bulletproof vests had outlived their life expectancy.
Internal affairs complaints dating back 12 years sat dormant, and police lacked the computers to run background checks on suspects.
But local law enforcement authorities argue that about 75 percent of the island's murders are drug-related, and the drugs come in by air and sea - which is federal jurisdiction.
After complaints last year from the governor and the island's representative in Washington, the feds began to take notice.
The Department of Justice teamed up with island prosecutors and police to create the Illegal Firearm and Violent Crime Reduction Initiative. In July, Department of Homeland Security Secretary Janet Napolitano visited the island.
"She looked me right in the eye and said, 'We're going to help you,' " Pesquera said. "I don't think she's blowing smoke."
The new cutters from Miami were lent to Puerto Rico, and employees for various federal agencies were deployed on temporary stints. The Department of Homeland Security launched task forces for drugs and guns coming in by mail and cargo.
By October, DHS said coordinated operations resulted in the seizure of more than 16,000 pounds of drugs and the arrest of more than 100 people.
"2011 was a bad year, no doubt about it," said Joseph Campbell, the special agent in charge of the San Juan FBI office. "There are so many gangs here, we have to prioritize which are the most violent, which are most negatively impacting communities."
More than 500 people have been charged in federal court with crimes ranging from carjacking to home-invasion robbery. Federal agents charged one man who robbed a Burger King restaurant of less than $100.
Suspects who use automatic weapons with obliterated serial numbers, have prior felony offenses, or rob a place of business are being charged in federal court. In some cases, prosecutors have applied the Hobbs Act, which makes it illegal to affect interstate commerce.
That means people who were wanted for multiple murders in Puerto Rican courts are doing serious federal time for firearms violations, and are being held without bail while they await trial. The idea is to skirt the Puerto Rican courts, which allow bail even in murder cases.
Experts say bail discourages witnesses from cooperating. Now, more victims are cooperating with authorities.
The results have worked beyond expectations: The five districts where the project was launched - San Juan, Carolina, Bayamon, Caguas and Ponce - averaged a 23 percent drop in homicides.
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"Some people could say that these are nickel-and-dime cases," said Jose Capo, the assistant U.S. attorney in San Juan who is overseeing the initiative. "The charges we are filing for the most part have nothing to do with murders or drug trafficking. We're looking for the most readily provable gun crime."
The theory is that the people locked up for robbing stores, homes and cars are largely responsible for the murders. Drug dealers carjack innocent drivers because they need the cars for drive-by shootings, and addicts invade homes to score money for drugs.
"They tend to be extremely violent," Capo said. "Law enforcement has been on the lookout for these individuals. They are suspected of multiple murders. We're able, in a simple case, to just get them off the street."
He cites the case of Carlos Morales Garcia, who was released this summer after serving 15 years of a 40-year sentence for a 1994 massacre that left six people dead. He had 57 prior convictions, including four armed robberies and seven attempted murders, Capo said.
He recently pleaded guilty to possession of an automatic weapon, and will face 15 years in federal prison at his January sentencing.
Pesquera said the federal task force is making so many arrests that the jails have to be notified in advance to bring in transport planes to clear out space for incoming inmates. Underscoring the lack of federal resources, the U.S. attorney's office had to borrow state prosecutors to handle the load.
"They have 12 of my prosecutors, 24 of my agents and 300 police. We have to loan to them. That explains itself," said Puerto Rico's attorney general, Guillermo Somoza. "They need to send more tools to patrol the air and water. Send planes or prosecutors or both."
Somoza acknowledged that his office filed charges in just 350 murder cases last year, even though 1,135 people were killed. With a clearance rate of less than a third, authorities are putting their hopes on Pesquera to turn around the troubled police department.
But since Luis Fortuno, the governor who appointed Pesquera, lost the November election, it is unclear how much more time Pesquera has on the job. His original agreement called for one year, after which he would return to his Port of Miami job.
With just a couple weeks left in the year, Puerto Rico has already logged almost 900 murders. This month, 14 people were killed, even as outrage over the latest gruesome killing sparked a movement that spread on social media.
"There are few places where you feel safe," said Luis Romero Font, who became a crime-fighting activist after the death of his son, who was killed in a robbery. "Puerto Rico has 4 million American citizens that have been forgotten by the federal government with regards to drug trafficking and crime. If this had happened in San Francisco, they'd have sent two divisions of the Army to resolve it."
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