A story starring Doctor Fate written by Harlan Ellison was mentioned in several different contexts in the early-2000s. Unfortunately, it never came to pass.
First mention was in the DC Comics in-house hype column "DC In Demand" in DC Books published with a December 2002 cover date. The column mentions "that the JSA will heat up further in another series with contributions by Harlan Ellison, Kevin J. Anderson, Michael Chabon, and other big names?" Then, shortly after the column was printed the series was announced, JSA All-Stars, with Michael Chabon attached (he wrote a back-up starring the golden age Mister Terrific). An article about the series on the comics news site Newsarama does mention Ellison though, stating "And while DC and writer Harlan Ellison were ultimately unable to work scheduling on a back-up story (as mentioned this month in the publisher’s new ‘DC on Demand’ information page), DC has still lined up an impression group of writers..." A story starring the golden age Doctor Fate was published in the series, but was written and drawn by Darwyn Cooke.
Then in 2002 Harlan Ellison was interviewed by the magazine Comic Book Artist. At the end of the interview he was asked if he would still occasionally write comics. He replied "I’m doing some right now. If I had not gotten involved in terrible, terrible, deadlines, I would have already finished a Doctor Fate I’m doing for [DC Comics editor] Peter Tomasi, that takes place back in 1940. In fact, it’s a story that takes place immediately after the banquet story in JSA Secret Files. But I was late with it, and he had to reassign it to someone else, so we have decided that we’re going to do… I can’t tell you exactly, but it will be a one-shot, killer project. A kind of dream of mine come true." This response was the first time the JSA story was specifically named as starring Doctor Fate, and he seems to imply it had grown beyond its original "back-up" length.
I have not found later references to the story.