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Originally Posted by Sabaku Kyu
If Root comes into conflict with Tsunade it raises big questions for Sai. He will have to make a choice between his new friends and the man who raised him. So far, Danzou has allowed Sai to remain in team 7, but does not like the emotions that are growing inside him. What will happen if Danzou gives him an order like, say, having to assassinate one of the Team 7 members? We don't know exactly how loyal Sai is to Danzou.
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Where is he anyway? I don't kow if it's related but Sai completely disappeared since they saw Deidara's last explosion. He wasn't there when they gathered at ground zero and he still wasn't there when they resumed their hunt after Sasuke.
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Well, Danzou founded Root so the organization as a division of ANBU so it has only been around since he came into power, which was probably some time after Sarutobi became hokage. Danzou himself is probably no older than Sarutobi was. The name "Root" might be a pun because Konoha means Leaf village and leaves come from trees.... which have roots.
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The Root member who gave Danzou's orders to Sai defined the organization by what make the power of Konoha's tree, hidden underground. So yeah the pun is quite certain.