The Tree of Life, Terrence Malick, 138 mins (12A)

Life, the universe and everything

You may emerge, like I did, from Terrence Malick's latest, The Tree of Life, scratching your head and wondering what on earth it was you have just seen. You may find it tricky to answer as simple a question as "Did you enjoy it?" Well, I suppose I did, in the sense that it absorbed, and intrigued, and delighted the eye, as every Malick film has done since his debut Badlands back in 1973. But pleasure, for any filmgoer, is necessarily bound up with discrimination, a need to examine how the parts work within the whole; and once you begin to unpick its admittedly beautiful fabric the thing no longer feels quite satisfying. It doesn't even feel properly finished.

How to approach it? With an open mind, preferably. Its enigmatic first image is that of a weird amber-coloured portal floating in space, or is it perhaps a womb ready to drop its psychic load on us, the unsuspecting audience? Gradually, a mood of loss emerges. To the forlorn strains of hymnal music, a mother and father learn of the death of their 19-year-old middle son. Their grief, seen but not heard, is characteristic of a predominantly pictorial narrative; murmured voiceover is preferred to dialogue, and imagery preferred to both. The picture leaps forward 40-odd years to the present, where the dead boy's older brother, Jack O'Brien (Sean Penn), is a grown man, lost amid the reflecting surfaces of his own architectural practice and remembering his 1950s childhood in the somnolent precincts of Waco, Texas.

That word "remembering" is central to Malick's creative method. Not for him the setting-out of a narrative, one scene after another. Instead, he recreates boyhood as it might be recalled by a fiftyish man, in sidelong moments, fleeting images, shuffled fragments of thought. Nobody films a more haunting breeze than Malick, and the way it wafts through the open windows of the O'Brien family home and twists the lace curtains seems like the current of memory itself. We are mostly in the company of young Jack (Hunter McCracken), a headstrong boy who loves his willowy copper-haired mother (Jessica Chastain) and fears his disciplinarian father (Brad Pitt), a working man of thwarted ambition and deep resentments. His tenderness towards his three sons always seems poised on the edge of violence. The dinner table, where eye contact is a provocation, becomes a volatile dance of dread. In time, young Jack's stirrings of hatred will turn to Oedipal rage ("Please God kill him").

But that is to run ahead of the film, which early on convulses into the mother of all flashbacks – about four billion years back, indeed, unto the very beginnings of the cosmos. It's a sort of nod to Kubrick's visions of the sublime in 2001: a Space Odyssey, whose visual effects creator Douglas Trumbull is also a consultant here. It sports through a kaleidoscope of primordial images: erupting volcanoes, molten rivers, creatures of the deep, waves of migrant birds. But where Kubrick took life to mean an essentially cold and ruthless force, Malick's is a mysterious ode to transcendence and the possibility of mercy, expressed in one extraordinary scene of a predatory dinosaur sparing the life of a wounded subspecies – a Jurassic perk, one might say. All are capable of compassion, even those equipped with razor claws and built like a 10-ton truck. Only a film-maker supremely assured of his own talent would dare to run together the intimate with the infinite, the beatific with the B-movie.

Then we are back to the wide lawns and tree-lined avenues of Waco, and a slow darkening of mood. The patriarch looms closer in the frame, the anger with his lot emerging in his harsh treatment of Jack. Malick understands how to use Pitt's swaggering physical presence, all the soft edges gone; the leanness of the dialogue suits his character's brooding inarticulacy. As young Jack, Hunter McCracken is wonderfully cast, his innocent round face holding the bud of something mean and sly. We see how he apes the bullying ways of his father when he's messing about with his younger brother (Laramie Eppler, a lovely mini-me of Pitt) but also his instinctive seeking of his mother's wing in moments of crisis – the arrest of a man on the town's main street is another of those never-to-be-forgotten memories. At one point Jessica Chastain is so ethereal she actually levitates, like an angel, and again we sense the troubled spirit of Oedipus in the longing gazes the boy directs at her. "When did you first touch my heart?" muses the older Jack, and we can't tell if he's mentally addressing his mother, or nature, or God. Or all three at once.

In fact, the older, soul-stricken Jack is the film's problem. Most of the story, after all, is going on in his head. Penn, wandering over barren landscapes at the end like an escapee from a sci-fi movie, projects some unresolved sadness that has driven him into solitude – but what is it? Surely not his brother's death: he died years before. The family's leaving Waco might have been a trauma, but again, it's a long time ago. Penn's middle years have gone missing. We have his boyhood, then a long unarticulated blank. I wonder if something major was lost in the editing, rather in the way that Malick's war epic The Thin Red Line (1999) finally stumbled into choppiness and incoherence. Could it be the number of editors employed here – five – who've spoilt the broth?

No, "spoilt" is wrong – "thinned" might be nearer the mark. Because for all its loose ends, its cosmic portentousness, and (let's be honest) its absolute lack of humour, The Tree of Life is a remarkably vital and sensuous piece of work. Visually the film nods through its influences – Hopper, Andrew Wyeth, William Eggleston's photographs of the everyday Southern US – yet its cumulative force is completely sui generis. The music, mostly yearning passages from moderns and greats (Mahler, Berlioz, Brahms, Holst), is also artfully arranged, filtered through Jack's recalling his dad's love of classical music. It is of a piece with Malick's rapt tribute to nature and the universe, to the strange grandeur of being alive. Nobody else could have made it. Few would even dare to try.