After "Asking Jeeves", I've found two posibilities for leaders in our time frame. Most of the Hojo Clan we're in power before the Sengoku time frame.
Hojo Ujiyasu lived from 1515 to 1570. He fought many battles against the Uesugi, Imagawa, the Takeda, the Ota, the Mogami, and the Ashikaga Families. I could not find any more info on him.
Kotaro Fuma
During the Tokugawa Shogunate one famous ninja leader, Fuma Kotaro, proved rather effective in his subversive activities.
Fuma Kotaro: Fuma Kotaro was the fifth generation jonin head of Fuma Ryu Ninjutsu. His ryu worked in support of Odawaras Hojo family, specialising in Guerilla tactics. Fuma Kotaros most famous battle was in March 1581, when troops of Takeda set up their fortress in Ukishimagahara, and the Hojo set up camp across the Osegawa river from them. The Fuma group crossed the river and attacked the Takeda group several times at night, and drove the Takeda camp into disorder with ninja tactics. By the time of the Tokugawa Shogunate, the Fuma Ryu had degenerated into a gang of pirates operating in the Inland Sea. Fuma Kotaro and his followers are believed to have been responsible for the death of Hattori Hanzou in 1596.
Hanzou eventually died during a battle against the Fuma ninja, in 1596. Their leader Fuma Kotaro was an expert in striking Tokugawa's installations and causing great damage, so Hanzou was ordered to kill him. Hanzou ordered the construction of a fleet of large boats, armed with heavy cannon, as he knew the Fuma ninja had only a few light boats with little or no arms. When the fleet was completed, Hanzou led the fleet around the seas to scour the Fuma ninja. Off the Suo coast, the fleet came across a small group of Fuma boats. The fleet manoeuvred to get within range, and then laid down a steady barrage of fire. All of the Fuma ships was destroyed except two which had stayed out of range. One boat was on fire, and appeared to be disabled. Hanzou ordered his gunboats to move towards the boat slowly so that a concerted barrage could finish off the ship. As they were manoeuvring, the tide changed, drawing all the boats into a narrow channel. Hanzou gave the command to begin evasive action, but then it was discovered that all the gunship's had had their rudders destroyed by Fuma Ninja using underwater techniques. Hanzou ordered the gunpowder to be dumped into the ocean, but there was insufficient time for this, so the men abandoned ship to find the water saturated with oil. When the ships collided, the ocean was turned into an inferno, killing Hanzou and his men. Fuma Kotaro stood on the deck of his command ship, the remaining one which had stayed well out of range and watched the death of the greatest ninja who ever lived.
He is also depicted in video games such as Onimusha 2 as a young Fuma ninja currtently working as a highly skilled theif for the Hojo.
Either of these would work.
Got tired of waiting for cz2 ( 
), plus I need time to think up a good Rise and Rule game...
).
I can't say the same for Mori though, mainly cuz I'm looking for a more influential clan... but you never know.
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