While pursuing alien criminals named Bacillus and Geega, Birdy and Tute infiltrate Earth under the cover of a rising Japanese idol and her manager. During one night on a routine mission to apprehend the said criminal, a civilian named Tsutomu Senkawa is used as a human shield. When Birdy realized that she killed him in an accident, she decided that the only way to save his life was to fuse her body with his in order to prevent him from dying. Tsutomu thought that it was all a dream until he found that he was unable to control his body one night after he was supposedly dead.

Birdy returns to her home planet Altaria to attend a trial of one of the smugglers that she had arrested. She and Tsutomu were questioned by a deity named Nejula Gate Altaria regarding Ryunka. Nejula reveals to Tsutomu that Ryunka is used as a nuclear weapon, killing off the inhabitants of a planet named Bilugema. While Birdy visits her hometown, a terrorist bombing destroys a convoy of vehicles.

An investigation team under Shyamalan's orders investigates the ruins of Sawajiri Village, even killing a policeman when Murota and Hayamiya decide to investigate. Birdy saves them from some of the armed men and fights the reconstructed marionette before she gets injured during an encounter with Gomez after defeating the marionette again.

Birdy and Tsutomu head to the Lost Bird to figure out a way to purge the Ryunka out of Sayaka's body. The two were able to do so, at the cost of Tsutomu's own body when he sacrificed it to allow Birdy to kill him again and purge the Ryunka parasite out of his body with Nejula in charge of containing it. The Japanese government had covered up the events as the JGSDF had mobilized in Roppongi. Due to the events, Sayaka loses some of her memories including her encounters with Tsutomu. Birdy once again merges with Tsutomu until a new body can be readied. Meanwhile, Gomez and his boss Revi had a conversation about whether Birdy is a threat, with Gomez telling Revi to take some precautions against her.

Birdy meets up with her childhood friend, Nataru, and they talk for a bit. They are interrupted by a girl in a wheelchair, who treats Birdy coldly. A second of the criminals is tracked down, and she pursues him for a bit, but he escapes only to be killed in a violent manner Birdy is not familiar with.

Birdy tracks down the illegal Virtual Reactor Chips purchaser, who is Nataru's father, Mr. Dusk. Dusk reveals he is a member of an Alterian freedom group, and that he helped disguise the escapees. Birdy goes after the nearest, but the escapees kidnap Dusk and interrogate him on the attacks on their number. He is murdered, which angers Nataru and upsets Birdy. Nataru kills another of the escapees, but not before learning Valic killed his father. Birdy promises to catch Dusk's killer.

The Escapees steal a nuclear weapon from an American Navy ship, and afterward Tesera tells them she will not contact them and wishes to remain as an Earthling. Capella is taken by a Federation Investigator after Irma convinces her to give up without a fight. Later, Nataru discovers a picture in Muroto's room of Tesera, and goes off to find and kill her. Muroto calls Birdy, and she finds Nataru just after he brutally murdered Tesera. She allows him to leave, and berates herself afterward.