Nechrom:well he is the only one that can link to the dark chakra years ago, so Danzo is sus of him and he will potentially recruit him as a root member, but Mc managed to injure the root making him realize that he is a threat
Honestly they can't take him it's one thing to sabotage your villige slightly and another to kidnap fresh chunin after the won the chunin exam and are therefore famous
He should be more cautious against Danzo and his minions more than ever. Because of that interaction, he’ll slowly get on their radar and he has to train and get stronger in order to be unrestricted and stand on his own against Jonin to Kage level ninja.
I'm really annoyed at the level of the Root shinobi. I understand that this is AU, but it's still pretty damn stupid. There are not many jounin-level shinobi in the villages, especially the elite ones.