Shimura Danzō was indeed notorious in the Shinobi World, but at first, none of that had anything to do with Shihōin Naraku!
Back then, Shihōin Naraku had only wanted to rely on his talent to keep growing stronger, ideally enough to stay alive in the dangerous Shinobi World!
But out of nowhere, Shimura Danzō had taken an interest in the talent Shihōin Naraku was gradually displaying and wanted to bring Naraku into Root to train him as a subordinate.
At the time, the head of Shihōin Naraku's clan was Shihōin Harumoto. As a veteran Jonin, he knew all too well how brutal life inside Root was.
The Shihōin Clan had finally produced a genius after so many years. Shihōin Harumoto would never allow Shimura Danzō to quietly drag Naraku into Root, leaving his fate unknown.
Under Shimura Danzō's harsh management, Ninja from the various clans who entered Root were bound by Cursed Seals and would only ever obey his orders.
The Shihōin Clan that Shihōin Naraku belonged to was a small clan with few members, and Shihōin Harumoto was its only Jonin to begin with. After his death, if the clan failed to produce another Jonin, then without a powerful protector, the Shihōin Clan might well fade away and perish at some unknown point.
For the sake of the clan's survival and Shihōin Naraku's safety, Shihōin Harumoto had stood firm against Shimura Danzō, then at the height of his power, and sought out Tsunade.
At the time, the deaths of her younger brother and lover had left Tsunade with no interest in taking students. She herself was living in a daze. Drawing on their clans' past friendship and his support for Tsunade's Medical Plan, Shihōin Harumoto had finally persuaded her to accept Naraku, making him part of the Hokage's faction.