Upstream Color is a difficult film to easily describe, as its editing style and plot are equally as discordant. It combines story elements such as pigs, body parasites and Henry David Thoreau's Walden, linked together in a means which only makes sense once you've seen the whole thing. But at its core, its about two broken individuals, attempting to move on from a supernatural event which changes the entire nature of their lives and everything they know.

We first meet Kris (Amy Seimetz), a woman who is drugged and hypnotized by a mysterious individual into giving away all of her savings, which leads to her losing her job and redirecting the course of her life. A year later, Kris encounters Jeff (Carruth) on a train, seemingly motivated to talk to him from a near-clairvoyant connection. They form a bond and soon fall in love, but eventually as they get to know each other it is revealed that their kinship goes beyond physical attraction, as it is motivated by forces beyond their comprehension due to the brainwashing incidents they have both been subject to. Kris and Jeff attempt to find a way to escape this intangible system of control, where their actions are connected to the life of another organism entirely, with only each other for guidance and support.