In a futuristic Tokyo, a young man awakens to find himself with no memories of his past. Behind him, a mysterious young woman named Elea appears. Handing him a pair of red glasses, she asks him to save the world! 

Three nights earlier, Jin encountered a mysterious man at a club, who informed him a boat would be arriving on the same night the UFO abduction took place. Upon reading the taxi driver’s statement, Jin decides to pursue the man.

Jin is approached in the park by a man offering work, which could make him a large amount of money in a short amount of time. While Jin declines the offer, the man leaves him his business card reading his name, “Tamaru”. 

Throughout the city, bodies are being discovered which have been transformed into mummies. DEUS order Agents Jin and K to investigate the phenomenon with Agent S, who has already discovered a common link between the victims.

Jin and K are ordered to investigate an alien crash site, but suspect that the survivor fled the scene. From the blood left at the crash site, Agent S determines the survivor as a known alien species who have been taken refuge on Earth after their homeworld was invaded by the ferocious Vo-Da aliens.

Jin, K and S are ordered to investigate a UFO crash site, but discover no wreckage. Soon after, people around the city are encountering a strange entity, which they have nicknamed the “Soul of Light”.

As Agent K investigates the appearance of a UFO in the sky, he is confronted by an army of aliens, the Vairo, who emit a deadly high-pitched scream.

Every night during a thunderstorm the phantom serial killer attacks, and it leaves behind a message written in blood: “Not Man”.

Peering through a pair of binoculars he discovers on a swing, Jin sees the moon turn red, and the hand of a strange creature. The agents are informed a woman in white will be targeted. Following her screams, K finds the woman confronted by a strange creature, who mutters the name “Mahiru” before ...

A news report states that Lake Nousu has dried up after a meteor impact, and a search is on for a man in the area who many by contaminated by radiation.

Jin is cross-examined by DEUS for trespassing an intelligence facility and aiding in Elea’s escape. Determined to discover the truth, Jin realizes he needs information from Elea.

Elea revealed the purpose of the Aqua Project was to secure a new energy source, but in the midst of the experiment a strange phenomenon occurred, and a gate to another world was opened.