Documentarian Alex Gibney has made a name for himself by examining the murky morality of our leaders and institutions, such as the Bush Administration’s war in Iraq (2007′s Taxi to the Dark Side), the scandals that brought down political figures (2010′s Client 9: The Rise and Fall of Eliot Spitzer and Casino Jack and the United States of Money, about lobbyist Jack Abramoff), corporate greed and corruption (2005′s Enron: The Smartest Guys in the Room) and the complicated ethical behavior of Wikileaks and its founder Julian Assange (this year’s We Steal Secrets: The Story of WikiLeaks).

But in 2008, producers Frank Marshall and Matthew Tolmach approached Gibney with the idea of following world-famous cyclist and cancer survivor Lance Armstrong as the seven-time Tour de France winner attempted a comeback. It was a chance for Gibney to both follow along inside the story as it unfolded and to tell an uplifting, inspiring story for a change.

Of course that film, originally titled The Road Back, was derailed in 2010 as long-standing allegations of performance-enhancing drug use and blood doping reared up again, eventually leading the United States Anti-Doping Agency to strip Armstrong of his Tour de France titles and ban him from cycling.

As Armstrong sat down earlier this year for an interview with Oprah Winfrey in which he finally came clean about his cheating, Gibney was working to restructure his documentary into yet another tale of a hero fallen and ideals betrayed: The Armstrong Lie.

The gripping result is a look at Armstrong’s past, how the doping accusations hounded him for a decade, how he continually and vehemently denied them, and how it involved his cycling team mates and his cancer-support organization LiveStrong. The film also incorporates a lot of Gibney’s original 2009 Tour de France footage as the filmmaker himself steps back and asks how he too got drawn into wanting to believe Armstrong, to believe in the comeback story.

I sat down with Gibney in Chicago last week to talk about The Armstrong Lie, about the many twists and turns in the film’s production, and of course about Lance Armstrong the man, who Gibney got to know well over the course of 2009.

The Armstrong Lie opens today in select cities.

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What originally drew you to this project in 2008?

Alex Gibney: I wanted to do something different, and I was approached by Frank Marshall and Matt Tolmach to do a film that followed Lance Armstrong’s comeback. It was interesting to me because I’m a sports fan, and comeback stories are interesting, and he’s the ultimate Comeback Kid, and I thought it would be interesting as a filmmaker to follow this interesting sport and this comeback. Great!

And from a deeper perspective, I was interested in Lance as a person because of his will and the inspirational aspect of it, and also what I suspected was a darker side—that this was somebody who’d do anything to win.

Do you think that will to win was what allowed him to stand behind his lies so long?

Gibney: I think the cancer story gave moral force to his lies. The cancer was real—no lie there, he almost died, and he came back from it and was a better athlete than he was before. So when people were challenging him, he could stand up and say, “How dare you suggest that I, as a cancer survivor, would ever dope?”

He’s on a crusade, so the end justifies the means. The police call it “noble cause corruption.” I think it did give the lie what Lance thought was a kind of moral force. It morphs into the ultimate shield, the ultimate alibi.

And on the other side, people want to believe him as long as they can because deep down they don’t want to hurt the LiveStrong cause or somehow damage the greater message about cancer survivors.

Gibney: How do you begin to tell people that actually you did kind of lie without seeing the whole edifice crumble. I think he felt once he went out on that limb like that, there was no going back.

Americans don’t know much about cycling, certainly not before Armstrong. Did the more obscure, outsider nature of the sport here make it easier for his American supporters to not question things?

Gibney: The easier thing for Lance was that he became far bigger than the sport, so that the sport either by intention or omission was honor-bound to protect him. That was the bigger problem. If you really want to understand doping, yes, you have to understand something about the sport.

But it’s enough to know that of the seven Tour wins, all but one of the people who shared the podium with Lance were popped for doping. That should tell you something.

I didn’t know anything about cycling when I started, but I learned a lot about how fantastic the sport itself is and how it works as a team sport—how team mates work with the director and lead rider to all move as one to push one guy onto the podium. From afar, it’s just a bunch of guys pedaling their bicycles, but there’s more going on.

But in terms of doping, you use your team mates to burn off the other teams’ riders. So Lance learned that if your team mates are all doping, they can burn off the other teams more effectively.

You often make films about darker subjects, but this was going to be such a different, more uplifting story. Then it turned on you.

Gibney: Initially I was disappointed, to be honest. But soon thereafter, I realized I was back on familiar territory, so I had a pretty good sense of where to go at that point. The great thing about documentaries is you owe it to yourself at the end of the day to make a film that’s compelling for people to watch and be moved by the story. But you also follow the story where it takes you, and if it takes you down a different path, you can’t  resist—you gotta go there.

Was this the first time you were covering a story from within as it happened as opposed to reflecting back on past events?

Gibney: It was the first time. Way back when I’d done some cinema verite films where you follow the story as its happening. That was one of the appeals of this film for me, to follow a story from the inside as it unfolded.

You end up inside the film, as a subject and participant in the events. At that point, how do you keep from wishing the story in one direction or the other?

Gibney: I wasn’t in the first version of the film—Matt Damon was the objective narrator. But in understanding the lie, part of what you have to understand is how people like me helped make it possible.

As a human being and a sports fan, you can’t help but root. So to understand what happened, I had to eventually become a character in the story, so you could understand the role played by the media and fans in terms of burnishing the myth. One of the reasons sports are so emotionally powerful instead of intellectual is that you feel it from the gut, it’s your team—you have identification, the team stands for you.

And with that emotional investment, it’s harder to believe a negative truth about your team. And when you finally accept that your hero has fallen, you tend to see him as the world’s worst villain.

Gibney: Europeans are more cynical, but I think particularly we Americans are more hard-wired to believe in perfect heroes. We want that perfect story, we want it bigger than life.

The Armstrong lie was so perfect—it wasn’t a little lie, it was that he never, ever, ever used performance enhancing drugs. He was the cowboy in the white hat, and now that we see it’s not true, he’s the black hat, the villain.

The film also shows how Armstrong rationalizes that he’s not lying when he says he didn’t cheat.

Gibney: His rationalization is a whole bunch of things mixed in together. Part of it is, “Everyone is doing it, so it’s bullshit, and I’m just part of the game. I’m not the only one.” Also for Lance, he had a bigger, more important story than everybody else did, with the Foundation and hundreds of millions of dollars for cancer support. He didn’t want that to go away.

And finally, I think Lance sensed in some fundamental way that people want the perfect story and he was gonna deliver it to them, giving people what they wanted. All those things became rationalizations for Lance in terms of making the lie so big. It gave him a force and at times made him actually believe that what he was saying was true, even if it wasn’t.

In his mind, he wasn’t cheating, he was just getting back up to a level playing field with everyone else.

There’s an old NASCAR saying, “If you ain’t cheatin’, you ain’t tryin’.”

As a film maker, how did you figure out what to do with your finished film The Road Back once legal events pulled the rug out from under it?

Gibney: We filmed this story as it was unfolding, so we had to go back over it. The advantage was it was a little like David Hemmings in Blow Up—he thinks he just has a photograph of Hyde Park, but he captures something he doesn’t realize. That’s how we felt—we’d captured something precious that we didn’t realize at the time: the lie in motion. We had this footage that we could now see in a completely different light.

And we captured the sport in motion, and you have to see that understand how the drugs worked and how the lie worked, but also to know the beauty of it, and how people get sucked up.

In hindsight, what does the film now tell you about Armstrong that you didn’t see there before?

Gibney: There are moments in the film when you see the real Lance, not the politician. At one point during the 2009 comeback, when he’d made up a lot of time and threatened to pass the leader on his team, I ask him if that’s a betrayal of his team and its designated leader, and he replies, “Betrayal? What are you talking about? I won the Tour seven fucking times. I deserve to have these guys ride for me.” That’s the unvarnished Lance.

At another point, when he was falling behind in his comeback, he says, “I’m sorry I fucked up your documentary.” I think I said, “Nobody fucks up my documentary.” [laughs] But I think his apology wasn’t just banter—it was his way of saying that people come to him because he delivers the perfect story and he’s sorry he didn’t deliver it this time

When I look back at the footage, I see that his whole 2009 comeback was partly an athlete wanting to show he can still kick everyone’s butts, and he needed that adrenaline that athletes need. But it was also him going back and trying to magically re-write the past. If he wins in 2009 racing clean, then in his mind he proves to everyone it doesn’t matter if he was doping in the past, he’s the greatest, so fuck you all. Or that he did it clean this time, so it proves he must have been clean in the past.

So what happens now to Lance Armstrong the human being?

Gibney: For those people who know Lance, you hope he comes to a moment where he understands that the most important thing in the world is not being recognized as a great athlete but as a good human being. People have the biggest problem not with what he did on the bike, but what he did off the bike. That’s what separates him from the rest of the cyclists.

But Lance isn’t spending a lot of his time thinking about that—he spending more time making arguments about why his title shouldn’t have been taken away and why he’s still the greatest cyclist of all time.

That famous and sometimes admirable force of will makes it so much harder to let go and reach acceptance.

Gibney: Lance is a fighter, that’s who he is. To do anything other than fight is tremendously hard for Lance, so that will be his biggest test.