Fune violently deposed the leader of a large group of raiders on Iki Island after the samurai were forced out. She established very violent punishments for those who defied her, ranging from outright executions to dying from exposure. She would become very successful and feared.
Fune did have a soft spot for her daughter, Toki. Tragedy would strike when Fune gave her daughter kusuri, a powerful medicine, to heal a broken arm which led to her developing a severe addiction. The last straw was broken after Toki, due her addiction, caused the deaths of several raiders during a raid. Toki should have been executed by Fune's law but she was instead sent away. Fune saw her behind a teahouse sometime later in a humiliatingly intoxicated state where she had soiled herself and was lying in a days old stench. Fune was furious and reluctantly left her there.
Fune would lead her raiders to fight the Eagle and her Eagle Tribe. She would be on her last legs until her lieutenant, Tenzo, arrived with a disguised Jin Sakai to defeat the Eagle. She recognized him as a samurai but was unaware he was the son of the infamous Kazumasa Sakai. Jin would build trust with her over destroying the Eagle's warship and retaking Fort Sakai. Fune would aid him in defeating the Eagle's forces in Kidafure Village.
She would soon be told of Jin's true identity but decides not to kill him due to the insistence of Tenzo that Jin is their invaluable ally who is not like his father. Fune meets the two after they successfully kill the Eagle but she is not quite done with the Ghost yet. She prepares a raid on an Eagle Tribe supply ship but neglects to inform Jin that they are truly going there to find an imprisoned Toki until immediately before the raid.
Fune and her crew face the Mongols which ends in her being victorious. She introduces Jin to Toki who is now in a vegetative from her severe kusuri addiction. Fune embraces her and informs Jin of their complicated history. As they leave, a mutinous pirate part of the raiding crew named Hachiro and his allies confront their leader. Hachiro desires revenge on Toki for accidentally killing her brothers and Fune for just sending her away. Jin and Fune dispatch Hachiro and his allies. After the battle, Fune thanks Jin for his assistance and goes to help Toki while Jin wishes her peace in dealing with her daughter.