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My friend, Isaac Hayes, died on Sunday, and his passing leaves many unanswered questions.

The great R&B star, actor, DJ, performer and family man, the composer of “Soul Man,” “Hold On I’m Coming” and other hits by Sam Moore and Dave Prater like “When Something Is Wrong with My Baby,” also was a member of the Church of Scientology.

Isaac was found dead by his treadmill, but conveniently missing from the wire stories was a significant fact: in January 2006, Isaac had a significant stroke. At the time, the word went out only that he had been hospitalized for exhaustion.

But the truth was, Isaac, whom I’d seen just a couple of months earlier when he headlined the Blues Ball in Memphis, was in trouble. Having lost the rights to his songs two decades earlier, he was finally making some money voicing the character of Chef on “South Park.” But “South Park” lampooned Scientology, so the leaders wanted Isaac out.

Push came to shove on Nov. 16, 2005, when “South Park” aired its hilarious “Trapped in the Closet” episode spoofing Tom Cruise and John Travolta. “South Park” creator Matt Stone told me later that Isaac had come to him in tears.

“He said he was under great pressure from Scientology, and if we didn’t stop poking at them, he’d have to leave," Stone said.

The conversation ended there. Isaac performed Chef’s signature song at the Blues Ball a week later with great delight. Although he was devoted to Scientology, he also loved being part of “South Park.” He was proud of it. And, importantly, it gave him income he badly needed.

But then came the stroke, which was severe. His staff — consisting of Scientology monitors who rarely left him alone — tried to portray it as a minor health issue. It wasn’t. Sources in Memphis told me at the time that Isaac had significant motor control and speech issues. His talking was impaired.

In March 2006, news came that Hayes was resigning from “South Park." On March 20, 2006, I wrote a column called “Chef’s Quitting Controversy,” explaining that Hayes was in no position to have quit anything due to his stroke. But Scientology issued the statement to the press saying Hayes had resigned, and the press just ate it up. No one spoke to Isaac directly, because he couldn’t literally speak. "Chef” was written out of the show.

Click here to read the March 20, 2006 FOX411

Isaac’s income stream was severely impaired as a result. Suddenly there were announcements of his touring, and performing. It didn’t seem possible, but word went out that he’d be at BB King’s in New York in January 2007. I went to see him and reported on it here.

The show was abomination. Isaac was plunked down at a keyboard, where he pretended to front his band. He spoke-sang, and his words were halting. He was not the Isaac Hayes of the past.

What was worse was that he barely knew me. He had appeared in my documentary, "Only the Strong Survive," released in 2003. We knew each other very well. I was actually surprised that his Scientology minder, Christina Kumi Kimball, with whom I had difficult encounters in the past, let me see him backstage at BB King’s. Our meeting was brief, and Isaac said quietly that he did know me. But the light was out in his eyes, and the situation was worrisome.

But the general consensus was that he needed the money. Without “Chef,” Isaac’s finances were severely curtailed. He had mouths to feed to home. Plus, Scientology requires huge amounts of money, as former member, actor Jason Beghe, has explained in this space. For Isaac to continue in the sect, he had to come up with funds. Performing was the only way.

In recent months, I’ve had conflicting reports. One mutual friend says that Isaac had looked and sounded much better lately at business meetings. But actor Samuel L. Jackson, who recently filmed scenes with Isaac and the late Bernie Mac for a new movie called “Soul Men,” told me on Saturday that Isaac really wasn’t up to the physical demands of shooting the movie. (Neither, it seems, was Bernie Mac.)

Sam Moore, who recorded those Isaac Hayes songs in the '60s and loved the writer-performer like a brother, told me Sunday when he heard about the death: “I’m happy.” Happy, I asked? “Yes, happy he’s out of pain.” It was one of the most beautiful ideas I’d ever heard expressed on the subject of death.

But there are a lot of questions still to be raised about Isaac Hayes’ death. Why, for example, was a stroke survivor on a treadmill by himself? What was his condition? What kind of treatment had he had since the stroke? Members of Scientology are required to sign a form promising they will never seek psychiatric or mental assistance. But stroke rehabilitation involves the help of neurologists and often psychiatrists, not to mention psychotropic drugs — exactly the kind Scientology proselytizes against.

What will come next, I’m afraid, is a wild dogfight among family members for Isaac’s estate. His song catalog (with David Porter) is one of the greatest in music history. Isaac lost the rights to his big hit songs in 1977. But thanks to something called the Songwriters Act, his heirs — whoever they are determined to be — automatically get the rights back as the songs come up for copyright renewal. I guarantee this will not be pretty. Isaac Lee Hayes has over 300 original compositions listed with BMI, from the Sam & Dave songbook to Carla Thomas’ “BABY (Baby)” to his monumental instrumental “Theme from SHAFT.”

None of this should ever take away from who Isaac Hayes really was: a great friend, a warm congenial man with a big heart and a big laugh. He had married again right before his stroke, and was very happy. If he hadn’t had the stroke, I am certain he would have recorded a new album. There was talk of it after the stroke, but nothing materialized. When we made and promoted “Only the Strong Survive,” he was a masterful musician with a great mind and a wicked sense of humor. His loss at 65 is simply way too early and very tragic.