Upstream Color tells the story of a woman (Amy Seimetz) who is abducted and hypnotized with an organic material harvested from a specific flower. When she falls for a man (Shane Carruth), the two come to realize he may also have been subjected to the same process. They search urgently for a place of safety within each other and struggle to assemble the fragments of their wrecked lives, unknowingly drawn into the life cycle of a presence that permeates the microscopic world.