In 2012, in the middle of a performance as an idol, Haruka Sawamura told a televised audience that the man that raised her, and who she views as her father, was a former yakuza named Kazuma Kiryu. Haruka left the stage, arrived in Kamurocho, and found Kiryu dying on the street. She got him to the hospital, but when he woke up he was arrested for the violence committed by the Omi Alliance and the Tojo Clan so that the Tokyo police could claim a victory by arresting someone who was considered a legendary yakuza.
Kiryu was voluntarily sent to prison, as he didn't want to cause the orphans at the orphanage he ran, Morning Glory, any trouble. Out of the idol business, Haruka tried to go back to the orphanage and her normal life. However, she decided to leave once she saw a tabloid article that claimed that her presence was proof that the orphanage was a front for the Yakuza.
In 2016, Kiryu was released from prison, traveled to the orphanage, and learned that Haruka had left and had never returned. He was told by the orphans that she had gone to Kamurocho to be with him.
Kiryu arrives in Kamurocho and tries to find information about Hakura from the mama, or manager, of New Serena. When she didn't have any information, he decided to ask Shin Akiyama. However, Kiryu discovers that Akiyama closed his loan office, Sky Finance. After asking people if they knew where Akiyama went, he discovers that he is in the sewer system.
Disguised, and once again a bum, Akiyama tells Kiryu that he had not seen Haruka. The two learn that an officer of the Saio Triad, Ed, followed Kiryu. He was after Akiyama because his loan office cut into the Triad's own profits.
Kiryu received a phone call from his detective friend, Makoto Date. Haruka had been in a car accident and may never wake from a coma. He also learns that she had protected a baby boy when she was hit, who was revealed to be her son, Haruto Sawamura.
Child Protective Services wants to take Haruto because Haruka had no known relatives. Because Kiryu is not her biological father, he is told he can not watch over him. Kiryu explains that both he and Haruka grew up in orphanages and he didn't want that for Haruto. When the CPS official still insists that he can't care for the baby, Kiryu takes Haruto and brings him back to New Serena. Luckily, Date convinced the officer that Kiryu could handle it, and vowed that he would be responsible if anything happened.
Haruka's phone was cracked, but the police were able to extract the location data. Kiryu learned that Haruka's previous known location was in Hiroshima, so he travels there to find out what caused her to come back to Kamurocho and to discover the identity of Haruto's father.