The world of Naruto has seen the introduction of quite a lot of rogue ninjas over the years. In fact, it can be said that the concept of rogue ninjas is one of the most exciting aspects of the series, because they make for very exciting villains. When it comes to the strongest of rogue ninjas, it is no surprise for the fans to know that the vast majority of them stem from Konoha.
In fact, Konoha has featured the strongest shinobi ever since the concept of Shinobi villages came into existence. Naturally, they would have the strongest missing ninjas as well, and over the years, Kishimoto has illustrated quite a few of them in a brilliant fashion.
Mizuki
When it comes to rogue ninjas, Mizuki is certainly the weakest of the lot from Konoha. Technically, Mizuki is only a non-canon rogue ninja. In the anime, he ends up being focused on quite a lot after the skirmish he has with Naruto. He ends up turning into a rogue ninja and his life is turned upside down due to these events. He isn't particularly good at anything, and even though he is bestowed with external powers, Mizuki ends up being dealt a pathetic fate.
Orochimaru
Orochimaru is one of the most ferocious rogue ninjas that fans have seen in the Naruto series. At one point, he was a loyal ninja of Konoha, however, his curiosities got the better of him and eventually, he conducted live experiments on humans.
When Hiruzen failed to persecute him for his actions, he escaped the village and from there onwards, became a rogue ninja. He plays the role of a primary antagonist for quite a significant portion of the series, and right until the very end, he was a very important character.
Kabuto Yakushi
Kabuto Yakushi was once a member of Konoha as well. He was taken in by an orphanage in Konoha and was then turned in to the ANBU, where he went on multiple missions for the village. Eventually, he joined forces with Orochimaru, who, in a way, manipulated him as well.
He then became a loyal follower of Orochimaru, following him all the way to the Hidden Sound Village. After Orochimaru's death, he became one of the primary antagonists of the series, having absorbed just about every power that he could find. It took two powerful Uchiha in Itachi and Sasuke to match him.
Itachi Uchiha
Itachi Uchiha is one of Konoha's mightiest ninjas. He was a prodigy of the Uchiha Clan. However, he was forced to live his life in exile following his massacre of the Uchiha. Of course, this was on Danzo's orders. However, Itachi had to pay for what he did as well. He infiltrated the Akatsuki for Konoha, and kept them from attacking the Hidden Leaf Village as well.
Technically, Itachi was still a good guy, however, he had to put up a facade, all for his village, and more importantly, his brother.
Obito Uchiha
Obito Uchiha was a brilliant shinobi and certainly a force to be reckoned with in the Naruto series. Although Obito once wanted to become the Hokage, the cruel twist of fate that was dealt to him in the Third Great Ninja War saw him follow Madara's footsteps. He was manipulated in a way where he decided that the way forward was to embrace the Eye of Moon plan and that is precisely what he did.
Obito became a missing-nin and he led Akatsuki from within the shadows. He was primarily responsible for the Fourth Great Ninja War and countless people died because of him.
Madara Uchiha
When it comes to strength, Madara Uchiha is certainly one of the strongest of the rogue ninjas. Technically, Madara was the one responsible for creating Konoha, along with Hashirama.
However, when he realized that the influence of Tobirama was going to be a problem for him, Madara's faith in Hashirama wavered and he decided to leave the village for good. Madara became a missing ninja and even attacked Konoha in an attempt to destroy it. This led to a fight between Hashirama and Madara in the Valley of the End, which the former ended up winning. However, Madara's plans did not stop there and he showed the fans why exactly he was the greatest villain in the entire series.
Sasuke Uchiha
When it comes to the strongest of the rogue ninjas, Sasuke certainly tops the list. Sasuke is one of the strongest characters to have lived in the Naruto world. He left Konoha after his face-off with Itachi in a quest for more power. He then went on to train with Orochimaru. At this point, he hadn't committed any crimes.
However, the more Sasuke gained powers, the more he descended into darkness. Eventually, after the events of the Kage Summit, he was branded a criminal and a rogue ninja. Sasuke helped in defeating the Akatsuki in the Ninja War, and he was pardoned for what he did to save the world.