Well, in fact, if I go with the games, the protagonist actually change every time. Masamune actually is just a protagonist in the first one, along with Yukimura. Second one is Keiji. Third one is Ieyasu (from what I've seen). Usually, the protagonist for each game has some kind of relation with the last boss of the game in some way, maybe except for the first one where they just want to win them.
In Basara 2, Keiji is an old friend of Hideyoshi. In Basara 3, Ieyasu formerly worked under Hideyoshi, but later betrays him. Mitsunari, who's the last boss of the game, is another follower of Hideyoshi and Ieyasu's old friend who he used to work with.
But well, for the manga, guess Masamune hooks everything then...-_-"
well Sengoku Basara 3 is finished, I don't know wich is the last chapter ! but in Februar there the third volume will be released wich contain a bonus chapter of 100 pages !!!! \o/
