The Naruto series has several incongruous aspects that have never been explained within the show, giving way to speculations and theories. One such element of the series is Kakashi’s Mangekyo Sharingan, an ocular technique that he had acquired long before the set time in part 1 of Naruto. It was revealed that Kakashi has a Sharingan in his left eye, though it was never disclosed that it was actually the Mangekyo.
The first time it was revealed that Kakashi possesses the Mangekyo Sharingan was in the beginning of Shippuden, when Kakashi used his Kamui to stop Deidera’s advance. The timing of this revelation is quite peculiar, as Kakashi should have had the Mangekyo in part 1 as well, yet he only chose to use it in Shippuden. This begs the question as to whether an actual in-universe explanation exists for this inconsistency or was it a result of hasty writing on the author’s part.
When Did Kakashi Obtain His Mangekyo Sharingan
Although it seemed that Kakashi had suddenly awakened the Mangekyo Sharingan in Shippuden, the reality is actually far from it. Since Kakashi’s Sharingan bears a link to Obito, the two awakened the Mangekyo simultaneously, when Obito witnessed Rin’s death. Her death triggered the awakening of the Mangekyo in both Obito and Kakashi, an event that took place when the two were around 13 years old.
While Obito had been witnessed using his Mangekyo as soon as he awakened it, Kakashi was never seen doing the same, not until the beginning of Shippuden. However, these events clearly depicted that Kakashi had indeed awakened his Mangekyo Sharingan a long time ago, though it remained unclear as to why he never used this all-powerful ocular technique.
Kakashi Wasn’t Strong Enough to Use His Mangekyo
The Mangekyo Sharingan is an extremely powerful technique, requiring immense chakra control and complete mastery over the base Sharingan. In Kakashi’s case, he was merely 13 years old when he awakened the Mangekyo and he had recently received the Sharingan from Obito, meaning he barely had any control on the base Sharingan itself. Under such circumstances, it's highly plausible that Kakashi’s body was never strong enough to be able to utilize the Mangekyo Sharingan and any of its abilities.
This is backed up by the fact that in part 1 of Naruto, Kakashi’s chakra would drain almost instantly after using the Sharingan, needing time to recuperate after every use. Since his Sharingan was perpetually active, a massive chunk of his chakra would be wasted simply to maintain the eye, let alone using any of its abilities. This is also indicated several times throughout the series, such as Kakashi’s fight with Zabuza, where he was seen in a weakened state after just one use of the Sharingan.
In Shippuden, every time Kakashi would use his Kamui, he would either pass out or need to rest for a prolonged period, as witnessed after the first time he used it against Deidera. In the Pain invasion arc, Kakashi even loses his life after a prolonged usage of the Mangekyo Sharingan against one of the Paths of Pain. This clearly depicts that the Mangekyo takes an extremely heavy toll on the user's body, and since Kakashi isn’t an Uchiha, his body had to suffer much more. It's highly plausible that Kakashi simply wasn’t capable of using the visual technique, as he needed more time to train to get used to the Kamui’s toll on his body – which he most likely did during the timeskip before Shippuden.
Kakashi Never Knew He Possessed the Mangekyo Sharingan
Another plausible theory that explains why Kakashi never used his Mangekyo before Shippuden is that he had never realized that he possessed it in the first place. This is somewhat likely from the fact that Kakashi passed out right after killing Rin and awakening the Mangekyo, as his body couldn’t bear the sudden surge in power. It's quite possible that Kakashi never realized what that surge of power was, as he could’ve easily confused it with the overwhelming emotions he felt after witnessing Rin being killed by his very hands.
The Mangekyo Sharingan is a secret even within the Uchiha Clan, as not many knew about the existence of this advanced form of the visual technique. Even Itachi had to tell Sasuke himself about the existence of the Mangekyo, as otherwise he had no source of finding this information. Therefore, it's impossible for Kakashi to even know that such a thing is possible to achieve with the Sharingan.
It wasn’t until he faced off against Itachi in part 1 of Naruto that he witnessed a Mangekyo Sharingan, finally finding out about its existence after suffering for days in the Tsukuyomi. It's likely that this is where he realized that such an upgrade of the Sharingan exists, and that he possesses one as well. However, he couldn’t utilize the technique right away considering the toll that it takes, meaning he had to train his body more – resulting in him using the Mangekyo Sharingan for the first time in Naruto Shippuden.