Lance Armstrong during the 2009 Tour de France. Agence France-Presse/Getty Images

Oscar-winning filmmaker Alex Gibney was in the midst of editing a two-hour-long documentary about Lance Armstrong's 2009 comeback to pro cycling—with the title "The Road Back"—when he heard the news that Floyd Landis, one of Armstrong's former teammates, sent lengthy emails to cycling officials providing details of the doping program on Armstrong's former U.S. Postal Service team.

Armstrong responded with powerful denials, calling Landis a liar. But then a two-year federal criminal investigation into doping on Armstrong's teams ensued, followed by a 2012 battle between Armstrong and the U.S. Anti-Doping Agency, with the agency releasing thousands of pages of its evidence against him.

In late 2012, Armstrong was stripped of all seven of his Tour de France titles, and in early 2013, he publicly acknowledged, on Oprah Winfrey's show, that he used banned performance-enhancing drugs and methods to win the event from 1999 to 2005.

Gibney had shelved his film, then was granted two more interviews with Armstrong, one with an Armstrong lawyer present. Gibney then recut the film, giving it a new title: "The Armstrong Lie."

The documentary, which features an interview with Wall Street Journal reporter Reed Albergotti, now explores whether Armstrong might have doped during his 2009 comeback. Armstrong maintains he was clean during the 2009 season.

Gibney recently sat down with the Journal to discuss the project. Edited excerpts:

What was the genesis of "The Road Back?"

Frank Marshall [Armstrong's then good friend] and Matt Tolmach [a fellow producer] had optioned "It's Not About The Bike" [Mr. Armstrong's 2000 inspirational autobiography]. And they were going to make a fiction film that was going to star Matt Damon. But they never got the script they wanted.

One of their problems was that they felt like Lance's story kept going on and on and on. And they were faced with how to capture a moment in time and yet he was still out there as a public figure—the real Lance Armstrong. In a way, it was kind of like the same problem as "Ali" had, which was a good movie, beautifully shot and rendered. But you know, Will Smith isn't Muhammad Ali. Muhammad Ali is better.

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Lance Armstrong—I don't care how good an actor you are—Lance may be one of the greatest actors of all time. Hard to beat that. So when Lance decided to come back in '08, he let them know and they said, "We want to shoot this."

When I first met Lance, I told him I knew very little about cycling. I knew he was good at it and that he won the Tour. I didn't know much about the Tour and I knew that there had been allegations about doping. My familiarity with the bicycle revolves around Schwinn. And I remember a three-speed from my childhood, and I had seen [the 1979 film] "Breaking Away."

How were you going to handle the doping topic?

In my first meeting with Frank and Matt, I mentioned the issue. I said, I would like to do this film but if I do this film, I presume you will give me license to investigate this aspect of the story. Because it wasn't like I was unaware of it. They said, "Yeah, that's fine. But in the main it's a film about his comeback." And I said fine. So I made it a rule for me…that anything I was going to do about the past had to have some connection to [the 2009 season].

My film was completed in late 2010 or early 2011. I was happy with it. But the more stuff came out, the more un-releasable it seemed. You're making veiled suggestions and there's no need for veiled suggestions because everything's out in the open. At some point, it seemed silly. In the wake of the federal investigation, being artful [about the doping issue] seemed silly. Because there's one moment in the film—which we preserved—where I ask Frankie Andreu in 2009, "Now '99…when you were on Lance's team, was there a team program?" And Frankie pauses, pauses, pauses and says, "I'm not going to go into all that." That was Frankie's way of saying, "Yeah, there was a team doping program" without saying it. That was originally in the film and that was our artful way of saying, "Guess what?" Now it looks so mild. You're looking at it thinking, "Why won't he come clean?"

What was on your mind after you read stories about Landis's sordid account of the doping program on Armstrong's team?

During the Tour of California 2010, I was still editing. But he comes out and it was like, oh my God. But still, Lance was on message. He was like, "Floyd is a liar. You know, he has lied before. Blah blah blah." So who knows how far that was going to go? But now there's a federal investigation that starts, and then spring 2011, Tyler [Hamilton] goes on "60 Minutes" and there's a mention in there of [Armstrong's longtime lieutenant George] Hincapie testimony. So suddenly Hincapie! Until all of this is resolved we can't really go forward. At that point we just put the film aside. It had been fully mixed.

We had been putting title cards at the end as something new happened [to update viewers on the doping scandal]. We finally realized we were going to have to put 20 minutes of cards at the end of the film. So we decided we're not going to release this version. We're going to wait until we know what's happening. The federal investigation was exploring all sorts of things that might have been explosive—conspiracy to distribute drugs. Nobody knew what the charges were. But suddenly, it wasn't maybe he had doped. It was a federal grand jury investigation. That gave us pause.

When I had a dinner with Armstrong in Austin after a screening of "My Trip to al Qaeda," he was talking about the federal investigation. He said, "Doping or no doping, what's the harm?" And I thought "Doping or no doping?! I didn't hear that come out of your mouth in 2009!"

What do you make of Armstrong's remark that he "did intend" to win in 2009 and "do it clean?"

I think that he is telling the truth. He intended to ride clean. But my belief is that he had an insurance policy. He has denied, even to me, that he did anything [to dope] in 2009.

Write to Vanessa OConnell at vanessa.o'