EXCLUSIVE: There’s bad news and good news on The Bourne Identity franchise front. First, the bad: Matt Damon definitely isn’t returning to reprise Jason Bourne in The Bourne Legacy, the next installment of the series based on the Robert Ludlum thriller series that Universal Pictures is hellbent on putting into production next spring for an August, 2012 release. The good: it turns out that even though Damon has been uninvolved in this new picture — he found out Tony Gilroy was directing when Deadline Hollywood broke the story — the film Gilroy is writing with his brother Dan has actually created some much-needed breathing room that insiders feel will make it easier for Damon to eventually come back for at least one more Jason Bourne turn. When Deadline recently revealed that Gilroy would direct the script he has been working on since last spring, Universal would only say the picture was going forward whether or not Damon came back. Actually, I’ve learned that Gilroy has smartly decided to remove the focus from Jason Bourne, and expand the franchise mythology. He’s creating new characters and will tell a different story about the parent company behind the murderous shadow government operation Treadstone, which brainwashed covert agents like Bourne and turned them into ruthless killers. I’m told the new protagonist will be another agent and probably a killer who went through experiences similar to Bourne’s or the character played by Clive Owen in the original Bourne. The plot accepts everything that has happened in the trilogy and factors it into the storyline. Because Gilroy isn’t replacing Bourne with another actor, he has made it possible for Damon to eventually return for a big paycheck reprise. Gilroy has also helped remove the ticking rights clock that put pressure on Universal to get another Bourne film into production. It is not at all a scorched earth situation between Damon and the studio.

So how did the new movie come about? Gilroy told me the momentum started slowly last spring, when he took a courtesy meeting to be polite to the Ludlum estate. He never thought it would lead to his third film as a director. “I told them, ‘I don’t have anything for you.’ I’d never seen the third movie, but went home and watched it. Awhile later, I had a slender idea, at least a way to attack the problem. We made a deal that was basically, ‘If you want to put me on for a couple of weeks to figure this out and go exploring in the hills, I can’t tell you what I’ll find but I’ll tell you where I’ll dig. And then I hit a vein, and ended up delivering way more than I thought. I came up with the whole thing and if it wasn’t a swinging idea, I wouldn’t have signed on to direct. It feels good, fresh, but quite honestly, a Bourne kind of movie. I brought in my brother Dan, we started off together as a team.”

Gilroy feels the loss of Damon. “Matt was completely not an option, and personally I couldn’t imagine trying to replace him. All the conspiratorial politics aside, these are very un-cynical, honest movies, and I don’t know another actor who brings more integrity and dignity, and a lack of cynicism to his work than Matt.” So Gilroy didn’t even try to replace him. “I’m not going to get into the plot, but you saw the other three films, you know everything that happened, and it’s not a dream sequence. What I can say is, you thought that was the whole world, but it was a small piece of what was going on. Ultimatum exploded at the end with people arrested. We deal with that as a reality, it has ramifications that echo out into the larger world. And of course, Jason Bourne is still alive and out there in the world. I don’t want to go beyond that, because the last thing I need is for every blogger to be second guessing.”

Gilroy, whose writing has essentially provided the creative backbone for the beloved Bourne trilogy, inspires confidence that he is onto something that can rise above a simple spinoff. The studio is hopeful the film will breathe fresh life into what remains arguably Universal’s most important film franchise.

The Bourne saga has long been filled with backstage acrimony and bruised egos since Gilroy wrote the first thriller. He famously did that without even reading the Robert Ludlum novel from which he only took the concept of an amnesiac killer who follows clues to figure out who he is. Gilroy glanced at the second book after the first film became a surprise hit, but didn’t base the second film on it. Doug Liman directed the first film, but it was widely known that producer Frank Marshall backstopped him, particularly in the later stages. Greengrass replaced Liman and directed the next two hits. Somewhere along the line, he and Gilroy stopped getting along, to the point where Gilroy turned in his draft of The Bourne Ultimatum and never looked back as he focused on making his directorial debut on Michael Clayton, getting Oscar nominations for script and directing. After The Bourne Ultimatum became a big hit, the pressure was on to craft a fourth film for franchise-hungry Universal, even though the Bourne storyline seemed to have been wrapped up nicely: the amnesiac assassin got his memory back and confronted his demons.

Damon and Greengrass went right back to work at Universal on the director’s passion project The Green Zone, a risky Iraq-set picture that was greenlit at around $80 million and went way over budget. Tensions were exacerbated after the studio hired scribe Josh Zetumer to work on the fourth film. Greengrass, who hadn’t been locked into another Bourne as a condition of Universal making The Green Zone, wasn’t pleased that the film was forming without his input. He formally withdrew last year. Damon, showing loyalty, publicly said he didn’t expect to be back as Bourne without his director.