Bacillus tries to locate and eliminate Birdy, while she, Tsutomu and Tute argue over the constant separate lives that they were trying to hide from the public. Tute gets wounded by Bacillus before he gave Birdy an Elemental Destructor capsule bomb to kill Bacillus and eliminate the threat of him killing an Earth-born civilian in Japan. Birdy mourns Tute's death when he can't heal his wounds from Bacillus' attack.

Nakasugi invites her friends including Tsutomu to her family village in the Sawajiri Village in Nagano. But on one evening, Nakasugi succumbs to the Riunka implanted on her by an unknown force who returned the renegade marionette back to her owners. A small number of Riunka explosions rattled the village, forcing local police and the JGSDF to mobilize.

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.

Senkawa and the journalism club go investigate a refugee camp. While Hayasumi is just trying to get a good story, Birdy is hoping to get a lead on another alien living in the camp. Two young children, Takumi and Marina, give the club a tour of the camp. They run away into the ruins so that they don't have to be separated, but get attacked by a group of thugs. Nataru, volunteering at the camp, goes after the children, but isn't strong enough on his own. Birdy arrives to rescue him.

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.