Birdy and Tsutomu try to cope with existing by sharing one body, but leading two separate lives. Birdy's commanding officer, Magius, informs Tsutomu that his original body's being restored and it will be some time before he can live outside of Birdy's body. Bacillus tries to eliminate Birdy by luring her into a movie shooting as cover. Keisuke Muroto tries to take photos of Bacillus and Birdy, but falls unconscious when he was knocked out by debris. A wounded Bacillus took over Geegar's Earth body as his first one was damaged from deterioration and from fighting Birdy.

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.

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.

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.