For the entirety of the original Naruto series, it seemed like Sasuke and Itachi were the only two living Uchiha, and their hatred for one another was one of the strongest storylines in the series. Itachi had seemingly killed the entire rest of the clan, leaving Sasuke alive so that he could one day kill his brother.
When Shippuden rolled around, some cracks in that presumption started to show. There were hints sprinkled throughout the series that there was a third Uchiha who still lived in the shadows, biding his time before he announced himself. Some of the hints were small, and others telegraphed the identity of the third survivor loud and clear.
9 Tobi Only Having One Eye Hole In His Mask
One of the biggest early giveaways of another Uchiha existing was Tobi's mere presence on screen during Naruto Shippuden. From the moment of his arrival, the question of why he only had one eye hole in his mask lingered unanswered.
Even back then, it seemed likely that he was Obito, especially considering how goofy he was. He acted just as an adult Obito would have, had he not endured all the pain he did. It was an outcome so obvious that most fans didn't think it'd be true. Even with the Madara swerve, the obvious answer ended up being the correct one.
8 Tobi's Ability To Phase Out Of Harm's Way
Beyond his outfit, Tobi also had the ability to phase himself through attacks. For most of the series, no one ever questioned it since Tobi seemed more like a comic relief character among the other villains of the Akatsuki.
The ability itself wasn't even fully realized until his battle with Konan, who'd analyzed how it worked and prepared for it. Once more of its capabilities came to light, its similar nature to what Kakashi could do was hard to ignore. Lo and behold, it was Kakashi himself who put it together.
7 The Downfall Of The Uchiha Clan Felt Too Convenient
While it made for a great story with Itachi and Sasuke, the entire Uchiha massacre felt too convenient. How did Konoha know the attack had wiped out everyone? Had there really never been any defectors from the village since Madara left after his battle with Hashirama?
It felt irrational that a group of people as fed up with being persecuted by Konoha wouldn't have had one or two people strike out on their own. Uchiha members were known to be emotional individuals, after all.
6 Itachi's Ability To Wipe Out An Entire Clan In One Fell Swoop Defied Belief
While it was explained that Itachi wiped out the entire clan by himself, the situation never made much sense. Sure, he was a prodigy and likely the second or third strongest Uchiha in existence, but him killing an entire clan of people who knew his techniques felt off. Even in the dead of night, there's no way he would have pulled this off as effortlessly as he did. He had to of had help from someone, and as it turned out, that someone was Obito Uchiha posing as Madara Uchiha.
5 The Timing Of The Kakashi Gaiden Flashbacks Were Fishy
The way Kakashi Gaiden worked as a bridge between the original Naruto and Shippuden felt like it was set up for Obito to be part of the story rather than simply being a way of explaining how Kakashi got his Sharingan. Unlike Rin, who was more of a side character in the episodes, Kakashi's relationship with Obito was the main storyline. Rarely does a character get introduced the way Obito was without them serving a grander purpose later on — and that's exactly what ended up happening.
4 Obito's Body Was Never Recovered After He Died In A Cave-In
During Kakashi Gaiden, Obito pushed Kakashi out of the way of a falling rock, saving his life. He even gave Kakashi his Sharingan as a parting gift before he died. As rocks continued to fall, Rin and Kakashi were unable to save him, leaving him to what they thought would be his death. But his body wasn't there afterward, forcing them to bury an empty casket.
Whenever a body isn't found, it always means that character isn't dead. It's one of the most used tropes in anime, right up there with the cloud of smoke always meaning a villain survived whatever attack the heroes threw at them.
3 Kakashi Unlocked The Mangekyo Sharingan Despite Not Being Of Uchiha Blood
Kakashi suddenly gaining the Mangekyo Sharingan by the time of Shippuden should have been scrutinized more than it was. At the time, most fans accepted it because it was a cool new development for a beloved character.
But it never made sense how he'd unlocked it, especially with what Itachi told Sasuke earlier in the series. This was the first real hint that Obito had to still be alive out there somewhere, because it was the only explanation for how Kakashi could utilize Kamui.
2 The Continued Mentions Of Madara Hinted That He Would Be The Final Villain Of The Series
One thing Naruto did very well is hint at the legacy of Madara and the Uchiha clan throughout the whole series. Both he and Hashirama were built up as untouchable god-like figures in the ninja world.
It's a classic decision in many long-running stories, helping build up the final bad guy before he inevitably reveals himself. Naruto even did it in a way that didn't make Madara some immortal being that lived far longer than he should have. It was a good job of foreshadowing until he was usurped by Kaguya at the last second.
1 Obito Revealed Himself As Madara Uchiha And The True Leader Of Akatsuki
The biggest giveaway was the outright reveal that another Uchiha existed when Tobi proclaimed himself as Madara Uchiha. The reveal was shocking and the start of two of the best story arcs in the entire franchise.
Having Tobi as the true leader of Akatsuki was mind-blowing and led fans to wonder how Madara was possibly still alive. It was the cherry on top of the other smaller hints that a third Uchiha was running around in the shadows and helped push the series towards its final showdown.