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 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 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.

Iruma, Birdy's contact on Earth for information, is kidnapped by the escapees to lure her into a trap. She escapes being nearly killed by a long-range gun and fights to a draw. She collapses before she enters the portal to her ship, however. Tsutomu has a weird dream, a blend between his own memories and Birdy's. This is when he discovers he is trapped in Birdy's body. He is thus forced to follow her schedule, including a signing some of his classmates attend, a photo shoot and a reality contest where he has to eat bugs. At the end, he learns that personality merging has begun.

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.

The School Festival opens where Hayamiya gives her piece on the disaster refugees. Nataru finds and severely wounds Gatoru before he and Moss escapes. Hoping to cut a deal with Revi Moss kills him but is rejected and decides to fight Nataru win or lose.

Nataru and Moss fight but Moss is nearly killed before being rescued by Birdy who attempts to convince Nataru to surrender and receive treatment before his Iksiola state kills him. He refuses and nearly kills Birdy before Senkawa switches in and convinces Nataru that being an Iksiola means more than just killing. Nataru relents and jumps back in time to the moment of the tower attack becoming the man who saves a young Birdy via a time-loop.