Every fan knows that the long-running Naruto series was full of twists, turns, and mysteries up until the very end. Whether a villain was concealing their true identity or a hero's backstory was lacking in detail, there were many large mysteries that kept fans guessing with theories and potential explanations. Eventually, these mysteries would be solved after years of mind games.
On the other hand, there were also certain mysteries from the series that were hinted at but never explained in full. Those mysteries were perhaps subtler than the ones that were uncovered, but that didn't take away from the fact that fans still wanted answers. Solved or unsolved, the many mysteries of Naruto definitely added an extra layer of story to the series.
10 Uncovered: Kakashi's Backstory
From his first introduction as Team Seven's leader, Kakashi had always come across as a mysterious character who kept his past to himself. It wasn't until the Kakashi Chronicles arc that his backstory was told.
In the arc, it was revealed that Kakashi was part of the Fourth Hokage's squad with his comrades, Obito and Rin, during the Third Shinobi War. In fact, most of Kakashi's beliefs and morals as a ninja come from what his comrades and the war taught him.
9 Never Did: Why Kakashi Always Wears A Mask
For the longest time, the biggest question on everyone's mind was in regards to what Kakashi's face looked like without the mask. As seen in his childhood flashbacks, he's worn a mask for as long as anyone can recall.
While Kakashi's face was revealed in a filler episode of Naruto Shippuden, fans never learned why the silver-haired ninja always kept his face concealed in the presence of others. Even when stepping into the hot springs, Kakashi refused to show his face to Sasuke or Naruto.
8 Uncovered: Pain's Identity
Starting in Naruto Shippuden, the Akatsuki became the central antagonists of the series. Their leader, Pain, was the one calling the shots, but his true identity was unknown for quite a while.
In place of the real Pain, the Six Paths of Pain would interact and fight with others on his behalf. At the conclusion of the Pain's Assault arc, Naruto finally came face to face with the real Pain, Nagato. After having a deep conversation about the fate of the ninja world, Nagato ultimately realized his mistakes and put his faith in Naruto.
7 Never Did: Hayate's Cough
After making it through the Forest of Death for the second part of the Chunin Exams, Naruto and the rest of the participants were met with the next exam proctor, Hayate Gekko. However, as he explained the next stage of the Chunin Exams, he was coughing quite a bit.
Hayate's cough and eye bags were noticeable to not only participants such as Ino and Hinata but also fans. Something was clearly wrong with Hayate's health, but he was killed by Baki before the illness could be mentioned or identified.
6 Uncovered: Itachi's Reasons
Itachi's motive behind wiping out the Uchiha Clan was exceptionally important for Sasuke to find out. For the majority of his childhood, Sasuke couldn't fathom why his older brother would do such a thing but decided to get revenge on him nonetheless.
After Sasuke finally succeeded in watching Itachi's death, Obito revealed the truth behind Itachi to the younger Uchiha. As it turned out, there was high tension between the Uchihas and Konohagakure, and Itachi was forced to pick a side. Ultimately, he chose to side with the village in order to protect Sasuke.
5 Never Did: Itachi's Illness
Like Hayate, Itachi had a mysterious cough that came out of nowhere. Whatever illness Itachi had, it was what ultimately killed him in his final battle against Sasuke.
Throughout the battle, Itachi coughed up a significant amount of blood but continued to act as though he was seriously going to kill Sasuke. In the end, Itachi was able to give his younger brother one last forehead tap before succumbing to his mysterious disease.
4 Uncovered: Naruto's Parents
Naruto grew up as an orphan, so the identities of his parents were initially unknown. That did not stop fans from coming up with one common theory as to who his father was. With blonde spiky hair and blue eyes, it was more than a coincidence that Naruto closely resembled the Fourth Hokage, Minato.
This theory would prove to be true in the latter half of the series. In addition, the identity of Naruto's mother was revealed to be Kushina Uzumaki, who happened to be the previous jinchuriki of the Nine-Tails.
3 Never Did: Naruto's Whiskers
Out of Naruto's many physical features, the whisker marks on his face stand out a lot. These lines might not be actual whiskers, but they are most likely associated with the Nine-Tails in some way.
Still, it was up for debate as to how those whiskers ended up on baby Naruto even before the Nine-Tails was sealed inside of him. A logical albeit unconfirmed theory was that the whiskers were caused by the Nine-Tails' chakra inside Kushina as she was pregnant with Naruto.
2 Uncovered: Tobi's Identity
Ever since Tobi replaced Sasori on the Akatsuki, there were many questions as to who this guy was behind that spiral mask of his. Little by little he hinted at his identity by dropping clues such as his Sharingan.
During the Fourth Shinobi War, it was finally revealed that Tobi was Kakashi's old friend, Obito. This came as a surprise because Obito was supposed to have died under a boulder in the Third Shinobi War. All this time, however, he had escaped death with the help of Madara.
1 Never Did: Hashirama's Cells
The First Hokage, Hashirama Senju, was often referred to as one of the strongest shinobi ever. Naturally, many other ninjas wished to be as powerful as him.
Therefore, ninjas like Orochimaru would experiment with Hashirama's cells on other humans as test subjects like Yamato. Other ninjas like Madara and Danzo acquired the cells through other methods, though the science remained a mystery as to how the cells worked and why Hashirama's face began to grow on them.