A trainer for Alex Rodriguez was shopping in Times Square with his wife and three young children one recent Saturday when he was followed into Toys “R” Us. A man working on behalf of Major League Baseball approached and handed him some paperwork. It was a subpoena to testify against Mr. Rodriguez.

Investigators working for Mr. Rodriguez, meanwhile, had a target of their own. They had received a tip that Robert D. Manfred, the league’s second-in-command behind Commissioner Bud Selig, had apparently been speaking indiscreetly about Mr. Rodriguez during a round of golf at Manhattan Woods Golf Club in West Nyack, N.Y. Enticed by the lead, Mr. Rodriguez’s investigators tracked down a caddie to learn what Mr. Manfred had said.

In the nine months since Mr. Rodriguez and more than a dozen other players were linked to a South Florida anti-aging clinic that is believed to have distributed banned substances to professional athletes, baseball officials and the Yankee third baseman have engaged in a cloak-and-dagger struggle surpassing anything the sport has seen. The extraordinary investigative tactics, playing out in multiple locations, reflect Major League Baseball’s resolve to prove one of its stars cheated, and that player’s determination to discredit baseball officials.

Witnesses for both sides in the pending arbitration proceedings claim to have been harassed and threatened. Some were paid tens of thousands of dollars for their cooperation. One said she became intimately involved with an investigator on the case. And some witness accounts have shifted, leaving each side scrambling to defend the sometimes inconsistent stories provided by former employees and associates of the now-defunct clinic, Biogenesis of America.