Naruto and Sasuke
One of the primary focuses of Shippuden is the relationship between Naruto and Sasuke. Both were outcasts who formed an unlikely bond thanks to their dreams of the future. The need for power was clear, and each set out along with Team 7 member Sakura and teacher Kekashi to reach their goals. Unfortunately, as the original series came to an end, it became clear that each sought power for very different reasons.
Where Naruto wanted to earn the love and respect of the village as well as protect his home, Sasuke wanted nothing but vengeance and control. As Shippuden progresses, the two begin to but heads more and more until Saskue finally takes his leave to join the likes of Ochimaru. This distance between the two friends plays a heavy role throughout the series as well as the end. Both are avoiding what must be done, and that building conflict will define the men they are going forward in life.
Both of the young men actually have a deeper bond that becomes clear nearer to the end of the Shippuden series. They embody the spirits of Indra and Asura, sons of the founder of shinobi. Those two are pit against one another in an eternal war, waiting for the cycle to be broken by two who are strong enough to put their differences aside.
