In 2019, following an uprising in the USA and a subsequent global nuclear war, humanity was decimated by a catastrophe called "The Maelström." A half-century after this cataclysmic event—to preserve humankind—the World Health Organization (WHO) has progressively assimilated worldwide political power and completely redefined society: people are now considered public resources and are guaranteed a happier life. The heightened development of medicine, nanomachine technology, and augmented reality promote this greater devotion to human health.

Suffocated by the excessive kindness of Japanese society, high school student Miach Mihie decides to oppose the societal values she considers dehumanizing before the health implant surveillance system WatchMe activates itself the day she turns 18. Miach plans to kill herself with two of her friends, Tuan Kirie and Cian Reikadou. However, Cian betrays the pact in disagreement with Miach's intentions, allowing Tuan to survive her suicide attempt, unlike Miach, who is declared dead.

Thirteen years later, now a high-ranking inspector of Helix—an organization affiliated with WHO to monitor military conflicts—Tuan is sent back to Japan after her drug smuggling activities in the Niger warzone are discovered by senior Helix inspector Oscar Stauffenberg. On her first day back to the country she tried running away from, thousands of people simultaneously commit suicide. Tuan is now in charge of investigating this wave of mass suicide and exposing the terrorist organization behind the unprecedented attack.

Harmony won the Platinum Grand Prize at the 2016 Future Film Festival held in Italy.

The film has been dubbed in English, French, German, Italian, and Russian. It was released on Blu-ray and DVD by Funimation on September 6, 2016 in North America and by Anime Limited on November 7. 2016 in the UK.