- "I care little for Nobunaga's ambition, but it must be fulfilled. All pieces must be in play before Ieyasu can claim his rightful place."
- ―Chaya Shirōjirō Kiyonobu to Hattori Hanzō, 1571.[src]
Aside from battling the Templars, the Japanese Assassins also aided the Tokugawa clan in unifying the land. To this extent, Hanzō killed the rival warlords Mōri Motonari, to aid Nobunaga's conquests, and Takeda Shingen, who held a Sword of Eden, which later wound up in Nobunaga's hands. Five years later, he killed the Templar warlord Uesugi Kenshin.
When the Tokugawa and the Assassins discovered that Nobunaga was to be attacked by his vassal Akechi Mitsuhide, Hanzō protected Tokugawa Ieyasu, while the Assassin Yamauchi Taka secretly killed Nobunaga amidst the chaos and retrieved the Sword of Eden. The Chinese Assassin Liu Yan then transported the artifact away from Japan.
In 1596, Hanzō was killed by a rival ninja, Fūma Kotarō. Suspecting that Nobunaga's successor and the new ruler of Japan, Toyotomi Hideyoshi, played a part in his death, Ieyasu tasked Yamauchi Taka with the investigation, which led to his assassination of Hideyoshi in 1598. The land then became divided between Toyotomi's loyalists, and Tokugawa's supporters, which included other Assassins like Mogami Yoshiaki and Yamauchi Kazutoyo. This led to the Battle of Sekigahara, in which Yamauchi Taka killed the general Shima Sakon to help ensure Tokugawa's victory, and consequently, the foundation of the Tokugawa shogunate.
In September 2012, the cell was being pursued by agents of Abstergo Industries. In response, they contacted the Assassin headquarters and informed them that they were going dark in order to lose their tail, scheduling to contact headquarters again on 30 September.
By 6 October, the cell had made contact with headquarters and informed them that they had not yet lost their tail and were going black until further notice. Eventually, the cell managed to escape from Abstergo.
In September 2013, their headquarters was attacked by a yakuza faction known as Onmoraki-Gumi, resulting in the deaths of several members, including Kenichi. His wife, Saeko Mochizuki, led the surviving Assassins in attack on the Onmoraki-Gumi in retaliation, and took over the organization, subsequently using it to blend the Assassins into the city and leading them as the Osaka Brotherhood's new Mentor.
On 17 December, at 9:47 pm, Assassin Kiyoshi Takakura was guarding the entrance to the new headquarters of the Osaka Brotherhood when he was approached by Gavin Banks and Emmanuel Barraza, who were investigating the deaths of Kenichi and the other Assassins in the destroyed bureau. When Gavin demanded to see the head of the Onmoraki-Gumi, Kiyoshi told him and Emmanuel to leave before he had to beat them, but Gavin then insulted his fashion sense and refused to go. Kiyoshi responded by punching him in the face and kicking him as he fell to the ground. Two of his fellow Assassins came out to watch and cheer him on. Fortunately, Emmanuel overheard the Assassins talking to each other about how Saeko would not like that kind of attention, as she had worked hard to keep the Brotherhood out of sight, and realized that everyone there was on the same side.
When Kiyoshi attempted to stab Gavin with his Hidden Blade, Emmanuel stepped in between them and caught Kiyoshi's fist in his hand, allowing it to be impaled. Emmanuel then asked Kiyoshi what the first tenet of the Creed was, stunning Kiyoshi, who responded it was "stay your blade from the flesh of the innocent". Emmanuel pulled out a dog tag with the insignia of the Assassin Order on it, proving he and Gavin were also Assassins. Kiyoshi retracted his Hidden Blade and apologized to Gavin and Emmanuel for attacking them.
On 18 December, at 1:03 am, Saeko met with Gavin and his cell of Assassins and laughed upon seeing Gavin's injuries, telling his cell that Gavin had always been troublesome. Over the next two days, Saeko exchanged information with Gavin. She informed him that the recent struggles against Abstergo and the yakuza had weakened the Osaka Brotherhood and drained their resources, with Japan's restrictive gun laws making it difficult to stay armed against their enemies. Gavin provided her with weapons his cell had procured in the Philippines and gave her the contact information for a supplier there. In thanks, Saeko passed on to Gavin an Animus headset her Assassins had stolen from a local Abstergo facility, and expressed her fears that the Assassin–Templar War was about to enter a new stage.
On 31 December, Saeko was invited by Eric Cooper to go on a tour of the Altaïr II. She disliked the disorganized state of the ship, and informed Captain Susan Drayton that the Japanese believed in starting off the New Year on a clean slate, which included having a clean house. Saeko enlisted the help of Susan and Eric in cleaning the ship and made homemade toshikoshi soba for them afterwards. Kiyoshi, who had accompanied Saeko aboard the Altaïr II to help the crew gather supplies for their next journey as well as to celebrate the new year, sparred with Emmanuel for three hours and managed to convince him to join Dr. Stephanie Chiu and himself at a local karaoke bar.
On 26 March 2014, Saeko received a message from Gavin's crew informing her of the destruction of the Russian Brotherhood and subsequently arranged to send weapons via the Philippine gun suppliers to a new cell of Assassins being set up in the country by agents of the Georgian Brotherhood.
In 2015, the Mentor Saeko Mochizuki sent teams into South Korea, North Korea and China to aid the local Assassin cells as part of the Brotherhood's global hunt for Álvaro Gramática, the Abstergo scientist who became a top priority when the Assassins learned of his plan to reconstruct an Isu's body using a Shroud of Eden, and his laboratory.
Allies and puppets