The film centers on Anemone, a girl who lost her father in a battle in Toyko seven years prior to the film's story, leaving her with only her stuffed toy Gulliver, and the AI concierge Dominikids for emotional support. Now she is a key part of a strategy by the experimental unit "Acid" to combat the seventh Eureka, "Eureka Seven," an enemy of humanity that has killed 2.6 billion people. Driven to the brink, all of humanity entrusts its hope to Anemone as she dives deep into the interior of Eureka Seven.