
Originally Posted by
danzo
One thing that came to mind when reading this is that Naruto being able to sense chakra when in sage mode was brought into the story when he first arrived at Konoha, and obviously this is intended the pay off for that little bit of writing.
But really, when Jiraiya was in sage mode, he had no such power. We know this because Pain used the chameleon to turn invisible and Jiraiya didn't know where he was as he used the barrier jutsu to relocate him.
Now, you could argue that it's because Naruto has better control over sage mode than Jiraiya which is why he's able to sense chakra, but in my opinion the truth is that kishimoto didn't plan it to work out like this when he was writing the jiraiya segment. Instead it's used as an instant plot tool for,
A) Naruto to find out that kakashi was dead, and thus motivate his emotions more.
B) Conveniently being able to locate the hiding Nagato
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