The Butterfly and Her Gale, this novel is set mostly in 2182, after the events of Guilty Gear, Guilty Gear X, and Guilty Gear XX, though it centers on Chipp Zanuff's life and thus has frequent flashbacks.
At the beginning of the novel, Chipp is chasing a bird as part of his ninja training for as-yet unexplained reasons. A flashback brings him back to when he first met his master, Tsuyoshi . At the age of 16, he was a mere street urchin, selling drugs. One day he's running from unidentified foes, drug-addled, and eventually he falls over, knocking himself out. When he wakes up, he's in a cave, being taken care of Tsuyoshi. Tsuyoshi rescued him, but also took his stock of drugs. Chipp, facing severe withdrawal, attempts to attack Tsuyoshi and take the drugs back, but Tsuyoshi merely defends himself effortlessly. In this matter Chipp tries for a month to kill Tsuyoshi and take his drugs back. Eventually Chipp realizes that his body is through the withdrawal and that he's following Tsuyoshi for a different reason. He finally asks Tsuyoshi to take him as an apprentice, and their master-apprentice relationship is born.
One day Tsuyoshi tells Chipp that he'll have to learn from the strongest creature in the forest. Chipp wonders if it's a bear, or even a Gear, but Tsuyoshi shows him a squirrel. He explains to Chipp that strength isn't just about being physically powerful, but also being fast, alert, and able to adapt to circumstances. With that, he collars the squirrel, lets it go, and tells Chipp to chase after it to complete his training.
Chipp flashes back to the present. There he is visiting Tsuyoshi's grave, and he vows to become President and find the scum who killed him. He also continues his training - this time by finding a beetle, tying a piece of string to its leg, then letting it go and chasing it. He chases the beetle for a few days, when it's eaten by a bird. Chipp, however, doesn't give up, and decides to chase the bird, as shown in the prologue. His chase eventually brings him to a small town. There he learns that the President of A Country (formerly the United States), a 17-year-old girl named Erica Bartholomew , will be visiting the town. Chipp doesn't really care, however, and it's only in the course of chasing the bird that he stumbles upon a group of assassins trying to take Erica out. One of the assassins screams "For the glory of Zepp!", but Erica recognizes it as a ploy - she makes an appearance, assuring the public that she's safe, and says that Zepp has nothing to do with the attempt.
Erica explains to Chipp that the A Country government is merely a puppet of a syndicate - the same Assassin Syndicate that sold drugs in Chipp's hometown, and the same Syndicate that had Tsuyoshi killed. Chipp exclaims that it's his goal to see that the Syndicate is ruined, and therefore says he'll be Erica's bodyguard until she manages to pass the law severing their ties with the Syndicate in Congress. Meanwhile another ship accosts the Presidential ship and demands that they hand Erica over. Chipp sneaks aboard and attempts to sabotage the engine, but he's stopped by a mysterious man in red named Volf - a man who says "So, it's Tsuyoshi's little pet." Chipp realizes that this man was the one who directly killed Tsuyoshi, and the pair fight, but Chipp soon takes off back to his own ship. Chipp flashes back to the day Tsuyoshi was killed. They were training on the mountains when they felt the Assassins coming.
Tsuyoshi demanded that they split up and they did. However, Chipp soon realized that the enemies he was facing were a mere distraction, and that the main force was going after Tsuyoshi. Days later he returns to the mountain and the cave, finding dozens of the assassins dead. Then in the cave, he finds a seriously injured Tsuyoshi, who first berates him for coming back for him, then tells him "I'm glad you're alive" before passing away. Back in the capital, Erica is meeting with Congressman Wu, who will be her representative in introducing the bill to Congress. However, in the next session, Wu doesn't introduce the bill. Chipp, angry, tracks Wu down and threatens to kill him. However, it's been a trick; Volf sneaks into the Presidential Office in Chipp's absence, and shoots Erica (with a decidedly black-tech gun). Chipp hurries back, realizing he's been tricked. Volf's subordinates are closing in, trying to finish the job, and Chipp's carrying Erica through the crowded streets. Suddenly, a tall figure with a bag on its head floats out of the sky with an umbrella... Faust fights off the assassins, then offers to patch up Erica. Chipp distrusts him at first, but realizes he has no choice. Erica recovers, but then realizes that they will probably try to pin the assassination attempt on Zepp once again (as Zepp is the only country known to support blacktech).
Though injured, she makes a public address once again saying that Zepp is not involved - and goes further by saying that she will be meeting personally with President Gabriel of Zepp in the near future. Chipp meanwhile tracks down Wu again, but Wu explains that he had received a letter from the Syndicate, telling him not to introduce the bill, or else they'd kill his daughter. Chipp threatens Wu again, telling him that if he doesn't introduce the bill he will kill his daughter. Later Erica meets with Ky Kiske of the International Police. She asks him for support in the upcoming plan against the Syndicate as well, and he says he will attempt to help in whatever means possible. Afterwards she meets with President Gabriel and Potemkin from Zepp. After Gabriel lays Chipp out flat (he explains that who needs a bodyguard when you can do things yourself), then the two begin a conference. During the conference, Erica receives a letter. It's from the Assassins once again, this time demanding that she stop meeting with Zepp, or else they'll kill the Director of the orphanage where she grew up - her foster mother, virtually. She is unsure what to do and asks for a recess.
Meanwhile the Director and Venom are playing a game of chess. Venom tells the Director that if Erica should make the wrong decision, he'll unfortunately have to kill her. The Director is calm, however. On the radio Erica suddenly comes on, saying that the conference with Zepp didn't go well, and then she screams - Zepp is shooting at the White House. Cut back to a few hours earlier. Erica asks President Gabriel to attack the White House. Gabriel, intrigued, asks why, when Erica says it's the only way to unify their two countries and shake off the involvement of the Assassins. Gabriel thinks it over, and agrees. With the attack by Zepp, Erica uses her power to call an emergency session of Congress at the Capitol. Meanwhile Volf has infiltrated, intending to finish Erica once and for all - but he's stopped by Chipp. The pair fight, but Volf pulls out an unfair advantage when he exposes Chipp to the very drugs he used to be addicted to.
The drugs weaken Chipp considerably, and Volf taunts Chipp by telling him that Tsuyoshi wasn't a ninja - he was just an Assassin like the rest of them. However, Chipp surprises Volf with his power of ki, and defeats him. He tells the badly injured Volf to run away before he changes his mind, which he does. Erica manages to get the law passed, and the Assassin Syndicate is seemingly crippled. Afterwards, Volf is running away when he's caught up by Venom - Venom doesn't take failure well, and he kills Volf. Meanwhile Ky meets with Erica and Chipp again - and he pulls out an International Police report on Tsuyoshi for Chipp. As it turns out, Tsuyoshi was indeed working for the Assassins - but he was actually an undercover agent for the Police. His cover blown, he ran away from the Syndicate, which is where he picked up Chipp. Erica asks Chipp if he still intends to be President. Chipp simply answers that he'll have to ask his master first, before disappearing. In the final scene of the novel, a bird is flying peacefully along... when Chipp appears, swearing at it, telling the bird that he'll catch it no matter what.