Terrence Malick has secretly been working on an extended version of “The Tree of Life,” which will be included by the Criterion Collection as a supplement to an enhanced special-edition Blu-ray and DVD release later this year.

The film, which won the Palme d’Or at the 2011 Cannes Film Festival, has grown 50 minutes of new branches — although roots might be a better metaphor, since the additional material focuses primarily on the lives of the O’Brien family (characters played by Brad Pitt and Jessica Chastain) and the backstory of Jack (Sean Penn), whose search for meaning in the wake of his brother’s death drives a transcendental quest unlike any previously depicted on film.

“Terry doesn’t see this as a director’s cut,” says Criterion president Peter Becker, who insists that the 139-minute theatrical version is the official “director’s cut” and remains the centerpiece of the Blu-Ray edition. “It’s a fresh view of the film that has a different rhythm and a different balance.

“There’s a kind of cloud of myth that surrounds ‘The Tree of Life,’ that somewhere there’s a long-lost five-hour cut that was never released. That’s not the case,” Becker says. “The film that he presented in Cannes is the film that he wanted to make.”

And yet, there could be no ignoring that the film continued to engage Malick even after its release: “These films are very much living things for Terry,” Becker says. The director — whose last feature, “Song to Song,” takes places in the Austin music scene — identifies strongly with the way musicians create, embracing the organic way their work is allowed to evolve over time. “A song has a life after it’s recorded — it is a beginning, not an end for musicians. Nobody expects Bob Dylan to go out on the stage and play the song the same way every night.”

Conversations between Becker and Fox Searchlight, which distributed the film theatrically, began as far back as Cannes 2011 about doing a special Criterion home-video release. When it became clear that Malick was interested in revisiting the movie, Criterion took the unprecedented step of financing an alternate version, overseen by Criterion producer Kim Hendrickson.

That meant tracking down palettes of original negatives in order to pull the scenes Malick wanted, scanning everything in 4K, grading the footage with cinematographer Emmanuel Lubezki to match the original film, and creating a full sound mix for the additional material. Malick himself dedicated the better part of a year to the project.

Alternate versions are nothing new for Malick or the Criterion Collection (which has released four of the director’s films, including a special edition of 2005’s “The New World” that includes three “variant versions”). But Becker insists, “We have never undertaken anything this extensive or this challenging, or anything that has taken this long to achieve or required so much effort on the part of pretty much every post-production craft. The only thing we didn’t do is go shoot new material,” says Becker.

As cinephiles’ imaginations race, it’s important to note: The expanded 188-minute cut doesn’t contain more effects shots, and the epic creation sequence remains untouched. But it restores material that Malick was exploring for the version that was shown in Cannes, including specific events and characters that were referenced only elliptically in the original film. Audiences will get specific insights into Mr. O’Brien’s painful upbringing, meet members of Mrs. O’Brien’s extended family, and witness a major natural catastrophe that serves as a kind of centerpiece for what Becker has been calling “the new version.”

At this stage, no theatrical release is planned. Criterion holds only home-video rights, “but Fox has been very supportive,” Becker says, “and we’ll see what the audiences demand.”