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.

Sayaka Nakasugi invites her classmates to her mansion for her welcome back party. Birdy investigates the site where she had killed Tsutomu in order to locate a marionette of non-Earth origin. Sayaka's maid Yoshio finds strange things have happened to her, which started to worry Sayaka's grandfather, Katsutoshi. Meanwhile, Nakasugi disappears from the Nakasugi Mansion after encountering a parrot, which was an alien being in disguise.

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 is informed of a break-out from an intergalactic prison, and manages to track down one of the rogue prisoners. Although she is ordered to apprehend the criminals alive, he was killed by the time she arrived on the scene. The only clue is a disguise chip, which dissolved the body.

Continuing the memory dive, Tsutomu learns more of the Central Tower attack and Birdy's part within it.