Because it’s risky to meet your heroes, I’m steering clear of the audio commentary on the new DVD of “Eternal Sunshine of the Spotless Mind” (Universal). The screenwriter Charlie Kaufman isn’t a hero, exactly. His prior films like “Adaptation” and “Being John Malkovich” have seemed clever and original but haven’t left a huge impression. This time out, however, he and director Michel Gondry created a major work of film that’s also a minor work of philosophy.

The genre is break-up-and-make-up romantic comedy, and its trappings are sci-fi, but the film’s cumulative effect transcends both. We first see shy, awkward Joel Barish waking up on Valentine’s Day, alone. On his commute he is seized by the desire to go to Montauk. He wants to meet a new girl, and on the beach, he does, a flame-haired free spirit named Clementine. In time Joel learns (as do we) that he actually dated Clementine for years, splitting up just days earlier. She visited the office of Lacuna, Inc., to have her memories of him erased from her mind. Distraught, he does the same.

It must be nice to be Mr. Kaufman, because everybody seems to want into his movies. He landed Jim Carrey, one of the biggest actors around, to play Joel, and Kate Winslet, one of the very best, to play Clementine. (Mr. Carrey’s muted performance is a common irritant among the film’s detractors, including my estimable colleague Nathan Lee. Me, I bought almost every syllable.) Mark Ruffalo, all mad-scientist hair and L-train glasses, plays the technician who spends a night in front of a computer, zapping memories like he’s playing a video game. To pass the time, he also gets stoned and dances all around the unconscious Joel with co-worker/ paramour Mary (Kirsten Dunst). This is a very funny movie.

Between zaps, the film pivots. Joel realizes he’s not really asleep: He’s inside his head in some kind of half-waking dream, reliving his memories as they’re being erased. He remembers the fights, the happy moments, and the happy fights, as when they take turns pretending to smother each other with pillows. As Clementine slips away, Joel changes his mind. He decides to fight the procedure, and she tries to help him. With the world dissolving around them, the film becomes a story of love-on-the-run. “You can run but you can’t hide,” says Ruffalo, clicking and puffing away.

Mr. Kaufman has Joel and Clementine comment on the scenes even as they relive them, a melancholy device that makes each scene affecting. Clementine warns Joel not to expect her to save his life. “I remember that speech really well,” he says. “I had you pegged, didn’t I?” she replies, smiling. As they talk, a bookstore – signs, books, everything – dissolves around them. Joel tries to beat the procedure by sneaking her into the most private parts of mind, the places he never let her see when they were dating. At the point of extremity, they open up to one another.

All the while, Mr. Gondry works to keep this from turning maudlin or sentimental. Surrealism, it’s been said, is the naturalism of dreams. This gives him a free hand to twist reality without seeming bizarre for the sake of being bizarre. He makes a minor fetish of houses and windows. Early on, Joel peeks into a house. We also see the exterior of Joel’s childhood house, both new and tidy, and when old and corroded. A couple that he visits fight while the guy is banging on a birdhouse. All of this creates a metaphor for the secure, permanent life together Joel and Clementine want, but are afraid to have.

In the interplay between the lead couple and the Lacuna technicians, Mr. Kaufman teases out another idea vital to the film. Ms. Dunst says adults are “a mess of sadness and phobias,” and that the procedure restores people to the innocence of childhood. But Mr. Kaufman doesn’t believe anything so simplistic, and neither should we. “Sometimes I think people don’t understand how lonely it is to be a kid,” Joel says. Memories aren’t the smudges that build up on life, they are life.

In the last half-hour, the language, the music, the visual system so carefully established begin to deliver an immense payoff. Joel and Clementine realize they’re reliving his last memory, the day they met at the beach. “This is it, Joel,” she says. “It’s gonna be gone soon. … What’ll we do?” “Enjoy it,” he says. Throughout the film, composer Jon Brion does a masterful job of warming up Mr. Gondry’s chilly visuals without slathering on the strings. Here, it sounds like he plays a composition backwards – a deft touch. Clementine convinces Joel to sneak into a beach house: “It’s our house just for tonight.”

The tone now changes. Though the other scenes have dissolved or vanished around them, this memory turns violent. The house begins to crumble. Sand fills up the stairway, sea water rushes in. The scene is lit by a single white light, like a deep-sea camera prowling around the Titanic. Why all the sudden gloom, the annihilation? The reason points to the film’s final level of meaning, Mr. Kaufman’s grandest metaphor.

If life is just memories, then memories are life; deleting memories means death. (Mark Ruffalo is not your typical grim reaper, but he’ll do.) Once you start looking for it, death imagery pops up at every turn: the smothering game, a killed bird, Joel’s painting that shows Clementine on a ship full of skeletons. They have run as far as they could, have tried everything they knew, but in the end still couldn’t escape. Even houses, which seemed so sturdy, have been destroyed. The film takes its title from Alexander Pope, but its moral is right out of Shakespeare’s sonnets: “nothing ‘gainst Time’s scythe can make defense.”

If you accept that Messrs. Kaufman and Gondry care as much about mortality as memory and heartache, the film’s final image takes on overwhelming poignancy. Joel and Clementine are playing on the beach at Montauk (not coincidentally, land’s end – the very tip of Long Island). They’re running through the snow, on the sand, by the sea – a triple image of transience, because snow melts, and sand doesn’t keep footprints, and the water will sooner or later take back the land. They have learned the lesson this film imparts with uncommon humor, maturity, and grace: To accept that such moments don’t last long – we have to savor them while they do.