There is a big confusion why Naruto could only use regular Sage Mode in The Last, but could still use Six Paths Sage Mode before in Shippuden and after in Boruto era. So this post is split into 3 parts:
- What is Six Paths Chakra
- How Naruto lost his Six Paths Chakra
- How Naruto regained it
What is Six Paths Chakra
Six Paths Chakra is the source of the Six Paths Powers, such as awakening the Rinnegan or Six Paths Senjutsu.
There are three ways to obtain Six Paths Chakra:
1. By mixing the chakra of Indra and Ashura (i.e. Living Madara)
2. By absorbing the chakra of all nine Bijuu and Gedo Mazo (i.e. Juubito)
3. By posessing the Yin or Yang seal (i.e. Hagoromo, Hamura, Naruto, Sasuke)
Six Paths Chakra is not the same as Hagoromo's (base/pre-sage) Chakra as it is only part of it. According to Hagoromo himself, his chakra not only consist of the chakra of Indra and Ashura, but also that of the Kyuubi. This explains why Hagoromo was not able to manifest in Madara's mind when he awakened the Rinnegan, and also why Sasuke was able to awaken Rinne Sharingan but Madara didn't.
Sasuke was also able to meet Hagoromo due to the small amount of Kyuubi Chakra he received from Naruto. And after he got Hashirama's cells from Kabuto, the Six Paths chakra mixes with the Kyuubi chakra to create Hagoromo's chakra. However after he exhasted all of the Kyuubi Chakra left in his body, he no longer see Hagoromo, even though he continue to replenish Six Paths Chakra.
This also explains how Hagoromo possessed one TSB prior to becoming the Juubi Jinchuriki.
Truth Seeking Orbs are awakened by Jinchurikis with Six Paths Sage Chakra. The number of Bijuu (Gedo Mazo included) corresponds to the number of TSB awakened.
At this point, Hagoromo's chakra already contains that of the Nine Tails.
Naruto with just base Six Paths Sage Mode had the fox-slitted pupils in his eyes, even without direct link to Kurama. This is because the chakra the Yang seal supplies contains Kyuubi chakra as well.
So instead of Six Paths Sage Mode, it could be more appropriately named Sage of Six Paths Mode (both translates to Rikudou Sennin Modo) as in "Hagoromo mode", the difference being the Kyuubi Chakra.
Lastly, this also explains how Ashura had a KCM-like yellow avatar that does not look like Kurama. By receiving all of Hagoromo's chakra, he possess the same element that makes Kurama the only Bijuu that has an avatar instead of Bijuu transformation.
How Naruto Lost Six Paths Chakra
Naruto first got Six Paths Chakra from Obito, whom extracted a small amount of Six Paths Sage Chakra from Madara. This is confirmed later by Kakashi when he got taken over by Obito.
Obito also extracted half of the Nine Tails for Naruto, which is how he ended up meeting Hagoromo.
When Hagoromo's right palm meets Naruto, the Sun seal, which symbolizes Six Paths Yang Power, was transferred to Naruto's palm.
When Kaguya uses Byakugan, she saw a massive amount of chakra from his right palm, which she identified as Hagoromo's Chakra. This means that the seal is the source of Six Paths Chakra for Naruto.
She also identified Sasuke's Chakra as Hamura's, which mean it is also an example of Six Paths Chakra.
However, after Six Paths Chibaku Tensei was cast, the two seals returned back to Hagoromo's palms. Even then, there are still residual chakra left inside their bodies, which is why he could still go into Six Paths Sage Mode afterwards in Valley of the End.
However, after the fight, Naruto used every bit of his chakra left in his body, to the point where even Kurama lost consciousness for supplying chakra.
Unlike Madara and Sasuke, who both cultivated Hashirama's DNA to produce Six Paths Chakra with their own cells, Naruto was given Six Paths Chakra directly by Obito. Without the DNA of an Indra's reincarnate, he is unable to replenish Six Paths Chakra by himself.
In the Boruto databook Zai no Sho, Sasuke was stated to be equal to Naruto by lore. Realistically speaking, Naruto who gained the other half of Kurama and Hashirama's cells is definitely more powerful than Sasuke who lost the Bijuu Chakra and his dominant arm. Only a significant difference, such as Naruto's lacking Six Paths, can possibly justify this massive gap in power.
How Naruto Regained Six Paths Chakra
As the progenitor of Chakra, the Ten Tails possesses all chakra, including that of Hagoromo. This is why all Juubi Jinchuriki was able to use Six Paths Senjutsu, and Truth Seeking Orbs.
The Juubi is also made up of the Chakra of 1 to 9 Tails and Gedo Mazo, the Ten Tails' husk.
All Tailed Beasts have an associated Kekkei Genkai chakra nature, a combination of two basic elements. The confirmed chakra natures are:
- Shukaku 1-Tails: Magnet Release (Wind + Lightning)
- Son Goku 4-Tails: Lava Release (Earth + Lightning)
- Kokuo 5-Tails: Boil Release (Fire + Water)
With 5 basic elemental chakra natures, there is a total of 5C2 = 10 Kekkei Genkai elemental combinations of chakra natures. Each of the nine Bijuu, including the Juubi husk, had a Kekkei Genkai. Also in the form of a God Tree, the Gedo Mazo got Wood Release, the combination of Water and Earth. It could even be manipulated by Shin: Jukai Kotan, a Wood Release Jutsu.
Together, the ten Kekkei Genkai corresponds to the ten Truth Seeking Orbs behind the backs of the Juubi Jinchuriki, including Hagoromo. Naruto lacking the Gedo Mazo is why he only had nine.
While he does not have the Juubi husk, he obtained the Wood Release Kekkei Genkai by infusing himself with Hashirama's cells, although the fusion does not happen right away. Naruto only gain its cellular regeneration when he was adult. By combining the Tailed Beasts' Kekkei Genkai and his own new Wood Kekkei Genkai, he can go into Six Paths Sage Mode.
This is also confirmed in the novel Shikamaru Shinden that Naruto is the Jinchuriki of the Ten Tails "in a manner of speaking". And because of that he possesses Six Paths Chakra just like Obito.
This also explains why Naruto no longer uses Six Paths Sage Mode in base, that is without going into Kurama Link Mode at the same time. (Although it is more of Bijuu Link Mode now since it links to not just Kurama anymore).
With just Wood Release and without the access to the chakra of the other nine Kekkei Genkai elements, he could only access his regular Toad Sage Mode.
What Naruto Never Regained
While Naruto can combine the Six Paths Chakra from his palm with the Bijuu chakra for elemental release, the chakra itself is by default, Yin-Yang Release, or chakra in its purest form.
Without Six Paths Yang Power, he no longer possesses Yin-Yang Release, even though he still get Six Paths Chakra from the Bijuu.
Similarly, Truth Seeking Orbs are also a Yin-Yang Release Jutsu, hence Naruto could no longer use them.
This is visually reflected on his cloak, that Naruto no longer have the "Six Paths" symbol on his back. This symbol also appears on the back of Hagoromo, Hamura, and both Juubi Jinchuriki. It also appears on Hagoromo's forehead, and the forehead of the avatar behind Hagoromo when transferring the seals.
Even Obito is able to awaken one Truth Seeking Orb after stealing just a little bit of Madara's Six Paths Sage Chakra. This is reflected on the "Sun" end of his Six Paths Sakujo, that he still has Six Paths Yang Power within him.
Meanwhile, Naruto has never seen with either ends of Six Paths Sakujo. This is because unlike the Juubi Jinchuriki, his Six Paths Yang Power comes from the seal, and he does not possess it within his own body.
In terms of chakra:
Sage of Six Paths
= Sage + Hagoromo
= Sage + Six Paths + Kyuubi
= Sage + Indra + Asura + Kyuubi
= 1-8, Gedo Mazo + Kyuubi