Shot on 16 mm film on a mere $7,000 budget, 2004’s “Primer” stands among the brainiest sci-fi movies ever made. But the technical story didn’t depend on a multi-million dollar Michael Bay budget — the director even filmed most scenes in one take. Jargon-laden dialogue made for a dense but rewarding script about a time-travel device that goes awry.

Nearly ten years later, former engineer Shane Carruth returns with a film even more puzzling, although the information lies in the experimental filmmaking instead of the script. Taking cues from Terrence Malick’s playbook, “Upstream Color” depends on the non-verbal cues of its actors and repetition of parallel imagery to drive the narrative.

But unlike “The Tree of Life,” Carruth aims for a darker, microscopic approach to the story. Equally disorienting and emotionally palpable, a man abducts Kris, an effects artist (Amy Seimetz). The mysterious figure uses a bioengineered grub to manipulate her. After a grisly surgery involving a pig, Kris recovers with no memory.

Eventually, she bonds with a trader named Jeff (Carruth), who shares a similar experience, and the two fall in love in the unspecified dystopia. Detailing the plot of “Upstream Color” poses problems because the film challenges audiences with fractured shards of information rather than a linear arc.

While the visuals remain arresting throughout the film, the experience feels dependent on your ability to empathize with the stone-faced acting. Many of Carruth’s lines feel stilted, but Seimetz drives the emotional arcs successfully. “Upstream Color” remains Carruth’s brainchild. And as the producer, writer, director, editor, cinematographer, composer and distributor — the film secures his position as a true autodidact. “Primer” wasn’t a fluke.

“Upstream Color” disorients, but for a true purpose. Shards of individual scenes and moments explore humanity’s loss of connection to the natural world. After abandoning an epic adventure, “A Topiary,” Carruth’s newest, represents his most personal work to date. The barrage of close-ups creates a singular tactile experience alongside a creeping electronic score.

Kris experiences the implanted grub moving throughout her limbs, more gripping than the chest-bursting scene in “Alien.” On screen, the digital and natural worlds somehow affect one another — close-ups show an illogical relationship with nature for Kris and Jeff. In one scene, the two recite “Walden” to each other in between swimming laps.

Ultimately, Carruth aims for Stanley Kubrick’s level of artistry. “Upstream Color” may fall slightly short, but the confusing experience gives darkly emotional strokes of genius that conventional movies fail to live up to. Carruth fills the movie with tantalizing visual riddles that reward multiple viewings. Even with its shortcomings and deliberate uncertainty, the movie marks the work of an auteur.