Alex Rodriguez received special treatment from the U.S. Attorney’s Office prosecuting Biogenesis founder Anthony Bosch, even though witnesses have “provided evidence that Mr. Rodriguez may have lied and may have allegedly facilitated Bosch’s illegal distribution of Schedule III controlled substances,” according to court papers filed in Miami Thursday.

That claim came in a motion filed by a lawyer representing a defendant in the sprawling federal case in U.S. District Court for the Southern District of Florida. Attorney Frank Quintero Jr. asked the court to compel prosecutors and Major League Baseball to comply with subpoenas prior to the Feb. 9, 2015 trial of his client, Lazaro Collazo, in order to help him prepare Collazo’s defense. Quintero included voluminous discovery material in his motion, and asked why Rodriguez, who received only limited immunity in the case, should get off scott free while Collazo and two other defendants, including A-Rod’s cousin, Yuri Sucart, are headed to trial.

Quintero further pointed out that statements made by A-Rod’s former lawyer, Joseph Tacopina, indicate that “another, yet undisclosed non-prosecution agreement exists (or communications to that effect) with Mr. Rodriguez and/or his counsel, as well as with other government witnesses.”

The court documents include Tacopina’s recent interview for New York magazine titled, “A-Rod’s Lawyer Declares Victory,” as evidence of a possible additional agreement. Tacopina references A-Rod’s immunity agreement in the article and says, “He didn’t get indicted… It’s over. Game Set. Match.”

According to Quintero, Tacopina’s statements show that Rodriguez has received “promises of non-prosecution by the Government,” since a limited-use agreement does not prevent the government from prosecuting a witness who lied to agents or if further evidence of criminal activity were discovered by investigators.

“Mr. Tacopina, who served as a prosecutor prior to practicing as a criminal defense attorney, would be aware that the immunity agreement conveyed to Mr. Rodriguez would not bar prosecution against his client under certain circumstances,” wrote Quintero, “such as for providing false information or information derived from other investigations/witnesses.”

The U.S. Attorney intends to “take no action against Mr. Rodriguez, instead making it known that they intend to rely on his testimony at trial,” Quintero wrote, adding that any additional immunity agreement would be subject to disclosure.

Some of the material in Quintero’s motion has already been reported by media outlets, including the Daily News, but much of it reveals the gritty details of the most extensive drug investigation in baseball history.

Attached to the motion are more than a dozen exhibits, including a DEA agent’s affidavit, proffer agreements, and testimony transcripts from Rodriguez’s 2013 arbitration hearing, where the Yankee slugger fought unsuccessfully to escape a lengthy Biogenesis doping ban handed down by MLB commissioner Bud Selig.

Quintero’s filing asks the court to compel MLB and the government to provide additional documents he says go to the heart of Collazo’s defense and explain any relationship between baseball and federal investigators. MLB has acknowledged responding to the government’s subpoenas for information gathered in baseball’s own investigation into Biogenesis but has said repeatedly that it got no help from the feds in return. In fact, MLB had to file a lawsuit in Florida state court in March of 2013 to compel Bosch and other Biogenesis defendants to provide evidence to help its investigation.

“MLB’s involvement in this cause did not cease after jumpstarting the DEA’s investigation,” Quintero wrote. “Instead, MLB has presumably steered, impeded and/or controlled the DEA’s investigation and the USAO’s prosecution thereafter.”

“We have no comment beyond there is absolutely no truth to those claims,” an MLB spokesman told the Daily News.

Thursday’s filing also includes testimony by Bosch’s former attorney, Susy Ribero-Ayala, during the Rodriguez appeal of his MLB suspension last year. Ribero-Ayala testified that she met with A-Rod and his lawyers Roy Black and Jared Lopez on Jan. 29, 2013, the day the Miami New Times posted documents linking the disgraced Yankee and other players to Bosch’s Biogenesis clinic. Rodriguez and his lawyers never denied the explosive allegations in the South Florida weekly paper during that meeting, Ribero-Ayala testified. But Rodriguez insisted they issue statements denying the steroid accusations, even though Ribero-Ayala was wary of issuing a statement denying Rodriguez and Bosch had been involved with performance-enhancing drugs.

“I think I said something about the fact that Lance Armstrong denied allegations, and it didn’t work out so well for him,” Ribero-Ayala testified, referring to the banned cyclist who had acknowledged in January, 2013, during a televised interview with Oprah Winfrey, that he had lied for years about his PED use.

Ribero-Ayala also testified that during that meeting with A-Rod, Black and Lopez, Rodriguez was the most vocal of the group, suggesting Ribero-Ayala release a statement on behalf of Bosch. “It was mainly Mr. Rodriguez,” she testified.

According to the exhibit, Ayala-Ribero first began representing Bosch on Jan. 27, 2013 — the day after the Daily News published a story saying federal agents and MLB were investigating Bosch and Rodriguez for their alleged involvement with performance-enhancing drugs.

The exhibits that accompany Thursday’s motion also include transcripts of the testimony that incoming MLB commissioner Rob Manfred (then baseball’s COO) gave on Oct. 17, 2013, when Manfred described how MLB investigators came to purchase Biogenesis records.

“There was an individual who called us,” Manfred said. “A gentleman by the name of Bobby — he identified himself as Bobby from Boca… We subsequently learned through investigation that the gentleman’s name was Gary Jones. And we eventually bought documents from Gary Jones.” Jones was later arrested for his involvement in a separate drug dealing scheme and recently pleaded guilty to federal drug charges.

In another exhibit, an affidavit signed by DEA agent Gene Grafenstein, there are details of a sizeable drug purchase made by a DEA confidential source on Dec. 14, 2012, and that the source made the purchase from Sucart and Carlos Acevedo, another Biogenesis defendant.

“The (confidential source) advised Sucart that the CS needed to purchase (performance-enhancing substances) in large quantities and that some of the intended recipients of the PES were high school athletes,” reads the DEA affidavit.