that it happened when Hanzou and Danzou tried to destroy yahiko and nagato's group....
I Agree with that part, he looked fine b4 Nagato summoned Gedo Mazo, we didn't get a look how he got out of this or if and how bad he was injured in that Battle. Also that was probably after the 4th's death (15 years ago if i remember correctly? Naruto is 16 and the 4th died when sealing the kyubi into his newborn son), so i'm pretty sure he didn't get injured fighting the 3rd, especially not fighting for the title of hokage.
Another possibility i thought of, is that his right side was crushed by Itachi after Itachi wiped out the Uchiha. As an act of revenge for making him kill his entire clan, which probably also included a bunch of innocent bystanders (like maybe sasuke's aunt and uncle? the one's he saw last b4 leaving for the academy that day). And also to get revenge on one of the men, that were responsible for the uchiha clan thinking, they were treated as "senju's dogs" which started the whole uchiha rebellion plan. It looks a little like maybe he got his right side burned completely by amaterasu.
But itachi, knowing that danzo in his own twisted way was trying to protect Konoha, spared his life and was satisfied with making sure danzo and the other elders understood the cost of harming sasuke after itachi left. Now that i think about it, maybe that was even his main reason for burning danzo's right side, to send a message to everyone who might harm sasuke after he left the village.
It would also be one explanation, why Danzo marked Sasuke as a missing nin so quickly. Although we - the readers - know that he wants to crush konoha (which noone except the "new" akatsuki group knows), until now sasuke hasn't really commited any acts of hostility against konoha (except fighting naruto to escape and joining akatsuki which has only recently become "public" knowledge). But he has done konoha some favors: he took down Orochimaru and 2 akatsuki members including itachi. But Danzo is afraid that sasuke might know the truth and is gonna finish the job itachi started. Also danzo is holding a grudge against uchiha for a long time and has finally the opportunity to get to the one uchiha who escaped his assasination plan.
At the Moment i can think of two possible Reasons why Danzo wants to get Kabuto b4 anyone else.
1. He wants the combined Medical Experiences of Kabuto and Oro to heal his right Side. And maybe he thinks he can even learn some of Oros Secrets from Kabuto, that he wants to keep for himself (keep in his own "capable hands" as he would probably put it)
2. He wants to make sure that Kabuto's Knowledge of Danzo & Oro working together doesn't become public Knowledge, because that could seriously undermine his position as Hokage (not only among the villagers and the other shinobi, some of which already know or suspect, but also among the feudal lords and the daimyo that gave him the position of hokage). After all it's the latest of many bad things he's done (supposedly to protect Konoha in his twisted mind) and it fits with what he did to sai and the rest of root's members (the seal on their tongue, preventing him from telling any of his ugly secrets to anyone else). Maybe he even took part in Oro's attack against Konoha during the chuunin exam, which Kabuto would most likely know if he did.
