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So in ep 380 of Shippuden, when Naruto and 2nd Hokage teleported everyone outside the barrier using the flying Ryjjin, the 2nd hokage said something about Naruto's shadow clone Jutsu. I couldn't quite understand what he was trying to say. Can someone please explain it to me?

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Earlier in the war, Naruto sent his clones out to each shinobi, and to each one, he gave them a bit of the 9 tails chakra. They obtained a basic red chakra cloak from that, which greatly increased their power. This chakra was linked back to naruto in much the same way as a shadow clone is.

When a shadow clone is created, the users chakra is split evenly between themselves and the clone. With 2 clones, each clone and the real body get a third of the total chakra. Likewise, any unused chakra left in the clone when it is dispersed, as well as any memories it obtained, are returned to the user near instantly. That is the connection between the user and the shadow clones. I believe this connection is forcefully upheld when new clones are created. In that respect, no matter how the clones are made, once a new clone is made, all the others loose a bit of chakra, and its given to the new clone so that they all have the same amount of chakra. I cant back that up though, because it is never stated, just implied by evidence. It however is the only explanation for the situation the 2nd hokage was describing, more on that later.

During the fighting, the Shinobi of the alliance lost their chakra cloak, because too much power was used. However (as later shown by the scene in question) the chakra was still there, it was just a small, unusable amount which was just enough to keep that connection alive.

Minato can only teleport those he or his chakra are directly touching. So, what Naruto did, was merge his chakra with Minato's, and had Minato's 9 tails give his 9 tails chakra. With the influx of chakra, it was then distributed to all of the shinobi alliance via that small unusable amount of chakra they all still had, the same principle as Shadow clones. When the main body got the extra chakra, it was evenly distributed to all of his "clones" which was every shinobi in the alliance. The merging of Naruto's and Minato's chakra let Minato teleport anyone connected to Naruto's chakra, and Naruto's chakra was, via the principles of shadow clones described already, connected to every single shinobi in the alliance, and only Sasuke and Jugo were excluded (excluding the other hokage), but (correct me if I remember incorrectly) Naruto grabbed onto them and that made the connection.

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Everyone using Naruto's chakra are linked to naruto as his shadow clones would. And when Minato connected himself with Naruto, he also indirectly linked himself with all the ninjas using Naruto's chakra.

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