On August 31, 1945, the Japanese battleship Yamato is destroyed in Operation Ten-Go during World War II. The Japanese government commissioned Iwami Shipbuilding to build the Yamato Mark II in the Onomichi area of the Jingaicho district in Hiroshima. After Japan surrendered on September 2, 1945, the Yamato Mark II was hidden in a warehouse under the sea and it was completed in secret. The existence of the completed Yamato Mark II was considered the secret of Onomichi.
In 2012, in the middle of a performance at the Japan Dome 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 property damage and 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.
Taega Saejima goes back to prison to serve the rest of his prison sentence. Kiryu also voluntarily went into prison, as he didn't want to cause the orphans at the Okinawa orphanage he ran, Morning Glory, any trouble.
Out of the idol business, Haruka returned to the orphanage and tried to resume her normal life. Six months later, she visited Kiryu in prison in Tokyo and learned that he could make parole in three years.
Haruka returned to the orphanage in Okinawa. However, she decided to leave once she saw a tabloid article that falsely claimed that her presence was proof that the orphanage was a front for the Yakuza.
With nowhere else to go, Haruka takes a boat to Onomichi in Hiroshima. The townspeople there immediately know who she is, but since they can tell she is actually a sweet girl, they are kind enough to not let on.
In 2014, she witnesses Yuta Usami of the Hirose Family, a second-tier yakuza group within the Yomei Alliance, beating a man with a camera. Yuta reveals that he was a paparazzi stalking her, which let him know that he knew her identity but also that he cared for her. After sleeping together a single time, Haruka and Yuta conceive a son together.
Shu Tatsukawa and Koji Masuzoe learn that Haruka is pregnant and try to convince her to have an abortion, which lets Haruka know that Yuta is the second in line of ascension to lead the Saio Triad. Toru Hirose, the patriarch of Yuta Usami's family, helps Haruka disappear without letting Yuta know either of her whereabouts or of the existence of his son.
Haruka used payphones to periodically call the orphans at Sunflower Orphanage, but the calls stop because she went into hiding when her son Haruto was born.
In 2015, Tsuneo Iwami and Katsumi Sugai convinced Jimmy Lo, the son of the Saio Triad's leader Big Lo, to stage a war between the Saio Triad and the Tojo Clan. As part of that plan, they burn down Little Asia. Big Lo is not happy with Jimmy's actions, but after learning that Jimmy got drunk and told Iwami the truth that Big Lo did not know the secret of Onomichi, the latter had no choice but to go along with the plan.
The fire led to the arrest of the top Tojo Clan leaders, Goro Majima and the Sixth Chairman of the Tojo Clan, Daigo Dojima. Their arrests allowed Sugai to assume the position of acting chairman of the Tojo Clan.
In 2016, Tsuneo Iwami determined that Jimmy Lo and Big Lo served their purpose, and hired Joon-gi Han, the leader of the Jingweon Mafia, to kill them. Jimmy Lo is killed, but the Jingweon Mafia is unable to locate Big Lo.
Now that Jimmy Lo was dead, Yuta Usami became the successor to the Saio Triad. Because Haruto is half-Japanese, he is considered an unworthy successor and the Saio Triad determines that he needs to be killed. Haruka and Haruto come out of hiding when Tatsukawa tells her to come to Kamurocho and gives her the false impression that he will help her, despite his orders.
In Kamurocho, Tatsukawa tried to get her into his car, but Haruka rightly didn't trust him. She tried to run away, but he accidentally ran into her with his car. She protected Haruto with her body and took the full force of the impact. Haruka and Haruto were taken under police protection at Touto University Hospital and Tatsukawa was killed by the Saio Triad for his failure.
Kiryu was released from prison. He traveled to the orphanage in Okinawa 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 arrived in Kamurocho and tried to find information about Hakura from the mama, or manager, of New Serena. When she didn't have any information, he decided to ask Shun Akiyama. However, Kiryu discovered that Akiyama closed his loan office, Sky Finance. After he asked people if they knew where Akiyama went, he discovered that he was hiding in the sewer system.
Disguised, and once again homeless, Akiyama told Kiryu that he had not seen Haruka. The two learned 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. The two defeated Ed and the Triad members that were his backup and left the sewer since Akiyama's disguise would no longer work.
Kiryu received a phone call from his detective friend, Makoto Date. Kiryu learned that Haruka had been in a car accident and may never wake from a coma. He also learned that she had protected a baby boy when she was hit. Kiryu is told the baby is Haruka's son, Haruto Sawamura.
He made a quick stop at the Tojo Clan headquarters where he learned that after Daigo and Majima were arrested, Sugai and Someya were installed in their place. Kiryu asked if they were involved in the hit-and-run that put Haruka in a coma, and when they denied it he warned them that he would come after them if he learned they were lying or if they got in his way.
When Kiryu arrived back at the hospital, Child Protective Services wanted to take Haruto because Haruka had no known relatives. Because Kiryu is not Haruka's biological father, he is told that he can not watch over the baby. 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 the baby, 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 on it. Kiryu learned that Haruka's previous known location was Onomichi in Hiroshima, so he traveled there to find out what caused her to come back to Kamurocho and to discover the identity of Haruto's father.
In Onomichi, Kiryu took Haruto to a snack bar called Snack Kiyomi and asked its mama, Kiyomi Kasahara, if she had any information about Haruka. Shortly after she said she hadn't, Kiryu is challenged to a fight by Tsuyoshi Nagumo, the captain of the Hirose Family because he has had a crush on Kiyomi since high school and thought Kiryu was trying to date her. Kiryu asked Kiyomi if she could watch Haruto, went outside, and won the fight against Nagumo.
Kiryu went back to pick up Haruto at Snack Kiyomi, and Kiyomi Kashara asked if he had anywhere to stay. She called a friend and arranged that Kiryu and Haruto could stay at Navy Apartments.
