Shikamaru is really smart. If anyone is going to figure it out and think deeply about Naruto, it's him.

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Secret

When Shikamaru finally figured out just what Naruto's big secret was he wondered if perhaps he got something wrong. Yet, everything added up. Naruto's birthday, the whisker marks, the odd swirl he'd seen on the other's stomach, the strange chakra, the slight transformation, and of course, the villagers hate.

It seemed strange that such a friendly boy could hold the terrifying Kyuubi. But then, it almost seemed fitting. Naruto must have had to endure some awful things growing up all alone.

Shikamaru speculated that Naruto was smarter than them all, being able to hide everything behind that disarming, happy mask.