November 03, 2008 12:00 PM

Out and about on Manhattan’s Upper East Side on Oct. 9, David Duchovny and Téa Leoni seemed like a couple who were putting some very public troubles behind them. “They looked happy,” says an observer who saw the couple in their New York City neighborhood more than a week after Duchovny completed a stint in a rehab facility for sex addiction. “They are such a nice family and get along great together.”

What goes on behind closed doors is clearly more complicated. A week later, the pair—who have been married for 11 years and have two children, daughter Madelaine West, 9, and son Kyd, 6—announced they had actually been separated for several months. “The couple had hoped to keep this separation private for the sake of their children,” a rep said in a statement.

Within days of that bombshell, a flurry of rumors about the troubled marriage of the Californication star, 48, and his wife, 42, who recently starred in Ghost Town with Ricky Gervais, hit the tabloids. Chief among them: that Duchovny had an affair with Edit Pakay, his tennis instructor, and that he had discovered revealing text messages on Leoni’s cell phone from Billy Bob Thornton, her costar in the upcoming movie Manure. “Billy and Téa are friends,” said Thornton’s rep. “But Billy does not text message, so the implication is not true.” And Pakay? “Ms. Pakay denied the rumors to me in person,” says Duchovny’s attorney Larry Stein, “and said in writing that such stories are ‘lies and deceit.'”

Whatever really caused their split, friends of the couple (who marked their 10th wedding anniversary in May ’07 by getting tattoos on their ring fingers) say both struggled to make the relationship work. A Leoni source says the allegations that she was unfaithful have been hurtful. “Téa is not the reason she and David separated,” says the insider. “Nor is her friendship with Billy Bob Thornton. To suggest any of this is her fault couldn’t be further from the truth.” As for Duchovny, a source close to the situation says, “He feels good that he completed rehab. David went in voluntarily, but Téa wanted it made public, which he did. He went to rehab to save the marriage.”

For now, Leoni remains with their children; Duchovny is living in Alpharetta, Ga., through November while he makes his upcoming movie The Joneses with Demi Moore. What next? “Everything’s up in the air,” says the source. “David’s obviously not thrilled about all the negative publicity, but for himself and his family, he’s doing his best to move forward.” Adds a friend of Leoni’s: “This is all very hard. But she and David are putting the kids first and they are the priority now.”

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