In its pursuit of PED-using players, MLB worked more closely with federal agents than anyone realized, according to new documents obtained by Newsday. They show that it was MLB that first informed the DEA about Biogenesis, even as the league sought to protect clinic owner Tony Bosch so his evidence could be used to suspend implicated players.

The federal wiretap affidavit obtained by Newsday indicates that the feds didn't know about Biogenesis until MLB approached them in September 2012, not long after putting together the pieces of a rash of failed drug tests, all with South Florida as ground zero.

"The focus of our interest in Bosch and South Florida picked up in the summer of 2012 when we began to realize that there were players who had connections, agents who were connected to those players, trainers who were connected to those players, businesses that were related to Bosch and others that we suspected were involved in the provision of performance-enhancing drugs," Rob Manfred said, according to a transcript of his confidential testimony.

Bringing in the feds allowed the full breadth of the Biogenesis ring to be uncovered—within months, the DEA had paid informants and undercover agents in place, and warrants to tap the phone lines of some of the major players. But the move also served as covering fire for baseball, which wanted to make sure the government wouldn't come in and disrupt MLB's own investigation, which even at that early date focused on Alex Rodriguez and his cousin Yuri Sucart.

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That meant keeping Tony Bosch out of the feds' crosshairs—and being able to offer Bosch leniency when the feds did come calling.

Though the agents obtained a pen register warrant for Bosch — which allowed them to record the phone numbers of calls going in and out — they did not tap his phone despite his role as a Biogenesis ringleader.

"My personal opinion is that MLB sought to protect Bosch," said attorney Frank Quintero Jr., who represents a Miami-area baseball coach indicted in the case. "He had already cut his deal with MLB. MLB knew there was going to be an arbitration hearing and wanted to make sure that his credibility wasn't further hurt."

[...]

Among the promises MLB made to Bosch in the agreement, which was obtained by Newsday, was that it would inform any law enforcement agencies of his role in "the important public policy goal of eradicating [PEDs] from professional baseball and request that such agencies consider his cooperation with MLB."

Bosch was offered a plea deal by prosecutors in exchange for his testimony against co-defendants.

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MLB told feds about players' ties to Biogenesis months before story broke [Newsday]