From birth, Big Lo's subordinates, Masuzose and Tatsukawa, secretly manipulated Yuta into learning Chinese culture in case his elder brother died, so that he could replace him and reign over the triad, per hereditary succession. Hirose eventually reveals that Yuta is Haruto's father, and the youngest son of Big Lo. Kiryu rejects the offer because of his role in framing Daigo. Likewise, Sugai and Someya want the Saio Triad suppressed, with the latter requesting support from Kiryu. Iwami and the Saio Triad also share the "secret of Omonichi". However, the hostility between the gangs became genuine after Tsuneo Iwami empowered the Saio Triad, only to later reject them and murder the eldest son of their leader, Big Lo. Kiryu also learns that Sugai and Someya initially provoked the war with the Saio Triad in the Tojo Clan's name, which included burning Little Asia, so that Daigo could be framed and arrested. Searching for Haruto's father, he meets prominent figures of the Onomichi Yakuza world: Takeru Kurusu, real name Heizo Iwami, chairman of the powerful Yomei alliance, and his son Tsuneo Iwami, CEO of his front company, Iwami Shipbuilding. Upon arrival, Kiryu befriends the local Hirose family, its patriarch Toru Hirose, and members Tsuyoshi Nagumo, Naoto Tagashira, Takaaki Matsunaga and Yuta Usami.
Learning that she has an infant son, Haruto, Kiryu travels with the baby to Onomichi, Hiroshima, retracing Haruka's steps. Upon release in 2016, Kiryu discovers that Haruka has disappeared, and later finds her in a coma after a hit and run incident. In his absence, an arson in Kamurocho's Little Asia district skews the criminal underworld's power balance: Daigo Dojima, Taiga Saejima and Goro Majima are imprisoned Katsumi Sugai and Takumi Someya usurp the Tojo Clan the Chinese Saio Triad, specializing in heihaizi human trafficking, rises to power in the area and the Jingweon Mafia resurfaces, occupying most of Kamurocho. Recovering from injuries sustained in the previous game, Kazuma Kiryu is arrested for past crimes, and willingly spends three years in prison, hoping for a peaceful life with his fostered children. Among them: Takeshi Kitano as Toru Hirose, Shun Oguri as Takumi Someya, Hiroyuki Miyasako as Tsuyoshi Nagumo, Tatsuya Fujiwara as Yuta Usami (Miyasako and Fujiwara both being recurring actors from Yakuza 3), and Yoko Maki as Kiyomi Kasahara, as well as other artists that have participated in the Yakuza series. Several renowned actors voice the characters in Yakuza 6.
Onomichi stands out from other cities in the series in that its name is the same as its real world counterpart, with the area featured in game being a recreation of the city's Shingai district. This game features the series staple location of KamurochÅ, Tokyo, as well as a new city, Onomichi, Hiroshima Prefecture. Additionally, unlike 0 and Yakuza Kiwami, Kiryu only uses one fighting style. Unlike Yakuza 4, Yakuza 5 and Yakuza 0, Yakuza 6 does not feature any playable characters besides Kiryu himself. Additionally, as is also later used in Yakuza Kiwami 2, the game categorizes experience into different types and the player can grant themselves various upgrades by using experience of the correct type experience points can also be earned by eating at restaurants, though doing this raises the hunger gauge which limits how much food the player can eat and reduces itself with time. It also features an advanced variant of Yakuza 5's Dragon Spirit Mode, called Extreme Heat Mode, where Kiryu becomes resistant to knockback as long as his Heat remains, and his combo finishers can turn into Heat actions that take out immense amounts of health. Yakuza 6 was the first game in the series to use the new Dragon Engine game engine (later used in Yakuza Kiwami 2, Yakuza: Like a Dragon and the spin-off Judgment), which overhauls the presentation and combat mechanics compared to past games. It is similar to that of other Yakuza titles with exploration mixed with arcade style beat 'em up combat with ragdoll physics. Yakuza 6 is an action-adventure game set in an open world environment and played from a third-person perspective.