Season 2

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.

Birdy meets up with her childhood friend, Nataru, and they talk for a bit. They are interrupted by a girl in a wheelchair, who treats Birdy coldly. A second of the criminals is tracked down, and she pursues him for a bit, but he escapes only to be killed in a violent manner Birdy is not familiar with.

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.

Birdy tracks down the illegal Virtual Reactor Chips purchaser, who is Nataru's father, Mr. Dusk. Dusk reveals he is a member of an Alterian freedom group, and that he helped disguise the escapees. Birdy goes after the nearest, but the escapees kidnap Dusk and interrogate him on the attacks on their number. He is murdered, which angers Nataru and upsets Birdy. Nataru kills another of the escapees, but not before learning Valic killed his father. Birdy promises to catch Dusk's killer.

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.

In an attempt to reverse the personality merging process, Tsutomu delves into Birdy's past. In this episode, he learns what it means to be an Iksiola, and how Birdy met Nataru.

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

Shouko catches Nataru and Birdy in an embrace, although only because of Birdy's clumsiness. As a result, she runs off out of the hospital, calling Nataru to come find her. But when she sees Birdy with him, she keeps running off. At the end of the episode, Nataru is shot.

Nataru jumps through time to just before he was shot, and manages to disarm and chase off Moss, injuring her in the process. She uses the injury to gain entrance to where Nataru works in the hospital, again trying to kill him. Nataru jumps through time, ending up a few days ahead of the event, his eyes turning red and bleeding in the process. Muroto finds him and takes him in. Nataru then asks Birdy to retrieve his medicine from his old apartment, and she discovers the blood from the fight.

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.