It seems a large portion of the base feels that PNJ was in full effect when Naruto re-entered BSM. I never saw it that way, here is my POV, hope it helps.
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I didn't find it to be an asspull or even PNJ at all.
As we know the Shinju tree does in fact absorb chakra, this however is not an instantaneous affect. It takes time, albeit a very short amount depending on chakra levels, to completely drain a shinobi's chakra.
Naruto was the first attacked by the Shinju and it used many branches to eradicate his accumulated nature energy as well as the Kyuubi chakra he was utilizing. Once the drain had begun though, his sync with Kurama ceased. He was no longer using the kyubbi chakra, in fact the sudden loss of that much chakra put him in an immobile state. He was unable to defend himself having lost his bearings, I liken it to having the wind taken out of oneself after a blow to the sternum, and he ended up being saved by the Sandaime.
Now I will explain how was able to re-enter BSM:
1. When first attacked by the Shinju, Naruto's extra chakra (Kyubbi+NE) acted as a shield of sorts.
The Shinju drained Naruto's Jinchuriki transformation as well as his Senjustu, and this elongated process shielded a good portion of Naruto's own chakra for a fair amount of time relative to the act. This barred the Shinju from having unfettered access to Naruto's own large chakra supply.
2. The Shinju did not absorb all of the Kyubbi's chakra.
Though Naruto unlocked his seal , Kurama's chakra and Naruto's are two separate entities. Once the Shinju began the absorption of Naruto's chakra, the link/syncing of their two chakra stopped. Naruto was not in a state to meld with Kurama, due to the near unconscious state he was left in after the Shinju attack/draining. As such he was not receiving an endless supply of chakra that was being transferred to the Shinju, he was left in a vulnerable, system shocked, energy zapped state that would result in his own pure reserve of chakra being further depleted. The latter however was negated due to the attempt of the Nidaime and success of Hiruzen in helping Naruto escape the absorption process.
3. Time passed/ Re-grasping of his bearings.
As we saw, instantaneously after the absorption process was stopped (i.e. the branches no longer coming in contact with Naruto), Naruto was able to discern and understand who had helped him. Quite different from his state not even one second before hand. After reuniting with his comrades away from the Shinju he came to even more, reacting to the effects of the Shinju's devestation.
In 647 we saw Naruto kneeling on the ground and supporting his own weight, no longer catching his breath or sweating as he was no more than 2 minutes before. Naruto had fully re-grasped his physical bearings and was taking in the situation and reacting i.e. crying. Then after processing what he saw and Sasuke giving him the notion that he too was ready to go, Naruto prepared himself for another assault entering BSM.
We saw how quickly Naruto gathered Nature Energy when using it in conjunction with Kurama's chakra and he did just that, however expediting the process by doing both transformations nearly at once instead of subsequently utilizing them.
Conclusion:
Take 1-3 and couple them with Naruto's vitality, stamina, life force, powerful chakra and you have yourself a logical conclusion.
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I hope my explanation helps, sorry if it ends up just being a waste of your time.
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I didn't find it to be an asspull or even PNJ at all.
As we know the Shinju tree does in fact absorb chakra, this however is not an instantaneous affect. It takes time, albeit a very short amount depending on chakra levels, to completely drain a shinobi's chakra.
Naruto was the first attacked by the Shinju and it used many branches to eradicate his accumulated nature energy as well as the Kyuubi chakra he was utilizing. Once the drain had begun though, his sync with Kurama ceased. He was no longer using the kyubbi chakra, in fact the sudden loss of that much chakra put him in an immobile state. He was unable to defend himself having lost his bearings, I liken it to having the wind taken out of oneself after a blow to the sternum, and he ended up being saved by the Sandaime.
Now I will explain how was able to re-enter BSM:
1. When first attacked by the Shinju, Naruto's extra chakra (Kyubbi+NE) acted as a shield of sorts.
The Shinju drained Naruto's Jinchuriki transformation as well as his Senjustu, and this elongated process shielded a good portion of Naruto's own chakra for a fair amount of time relative to the act. This barred the Shinju from having unfettered access to Naruto's own large chakra supply.
2. The Shinju did not absorb all of the Kyubbi's chakra.
Though Naruto unlocked his seal , Kurama's chakra and Naruto's are two separate entities. Once the Shinju began the absorption of Naruto's chakra, the link/syncing of their two chakra stopped. Naruto was not in a state to meld with Kurama, due to the near unconscious state he was left in after the Shinju attack/draining. As such he was not receiving an endless supply of chakra that was being transferred to the Shinju, he was left in a vulnerable, system shocked, energy zapped state that would result in his own pure reserve of chakra being further depleted. The latter however was negated due to the attempt of the Nidaime and success of Hiruzen in helping Naruto escape the absorption process.
3. Time passed/ Re-grasping of his bearings.
As we saw, instantaneously after the absorption process was stopped (i.e. the branches no longer coming in contact with Naruto), Naruto was able to discern and understand who had helped him. Quite different from his state not even one second before hand. After reuniting with his comrades away from the Shinju he came to even more, reacting to the effects of the Shinju's devestation.
In 647 we saw Naruto kneeling on the ground and supporting his own weight, no longer catching his breath or sweating as he was no more than 2 minutes before. Naruto had fully re-grasped his physical bearings and was taking in the situation and reacting i.e. crying. Then after processing what he saw and Sasuke giving him the notion that he too was ready to go, Naruto prepared himself for another assault entering BSM.
We saw how quickly Naruto gathered Nature Energy when using it in conjunction with Kurama's chakra and he did just that, however expediting the process by doing both transformations nearly at once instead of subsequently utilizing them.
Conclusion:
Take 1-3 and couple them with Naruto's vitality, stamina, life force, powerful chakra and you have yourself a logical conclusion.
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I hope my explanation helps, sorry if it ends up just being a waste of your time.