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 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.

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.

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.

Birdy fights with King Zero as Nejula corners Gelabu--whom ultimately commits suicide for his "pride" or "honor." Thanks to Birdy's way with words and the simple fact that King Zero's girl can't stand to see lots of people die, she detonates the falling satellite which was targeting the Union. Kashugeza turns out to be an undercover agent under Skeletsu's direction. Birdy is quite frustrated with the fact that Skeletsu tolerated the deaths of her fellow, innocent, Altarians in the terrorist attack in order to get a lead on King Zero.

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.

A string of murders with dead female victims with short hair and glasses leads Birdy to investigate them with Tsutomu. The culprit is revealed to be a rogue combat marionette, which is killing the victims as it thinks of them as the mother, the main programmer when the marionette was placed under her care. Birdy attempts to retrieve it, but is attacked by supposedly a Federation-based person with a guardian robot that attacks her to keep her away from acquiring the disabled robot.

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.

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.

Tsutomu and Nakasugi go on a date with Tsutomu received a kiss from Nakasugi herself. Meanwhile, Shyamalan meets with Sayaka's grandfather and kills him during the meeting. When Yoshie discovers his body, she thinks that Sayaka killed him, which activates the Ryunka in her body and evaporated her.

It has been confirmed: Nakasugi is the host for Ryunka. But Tsutomu wants to protect her, no matter what and so he takes control of Birdy's body when she tried to get close to Ryunka. Nejula knocks them out before their minds fuse completely. When they wake up again, Tsutomu has his own body back and needs glasses again. From now on, Birdy and Tsutomu go separate ways. When Birdy and Nejula arrive at Nakasugi's villa, she is already gone because she went to Tsutomo's place. To protect her from being pursued by her greedy relatives, Tsutomu leaves her in Shymalan's care. After that he discovers Shymalan's true intentions when Nejula confronts him...

Shymalan releases a recorded TV announcement, saying that he intends to wreck genocide on Japan to weed out the weak. The government, though slow, has begun to take steps to contain the Ryunka that is beginning to spread throughout the Greater Tokyo Area. Tsutomu, though advised not to go out of his house, decides to do so and save Sayaka. Nejula suggests that a faction of the Federation Police may have not decided to quickly respond to see the power of Ryunka. Muroto decides to help Tsutomu after he finds out that the ship is the Lost Bird, where Sayaka is held. Shymalan is killed when the Ryunka inside of Sayaka is activated, with a segment of the Japanese public. Birdy, meanwhile, is moving in on her own to stop the Lost Bird from moving any further.

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.