Well, a great plot might be that Naruto is framed as an assassination specialist by an enemy. So he has to clear his name while also dealing with the real assassins who are causing chaos. Maybe he teams up with some of his old foes-turned -allies, like Gaara, to figure out who's behind it all. They could travel to different hidden villages to gather clues and in the process, Naruto could learn new skills related to stealth and assassination, not to use them for evil, but to stop the real villains.
One plot idea could be Naruto being secretly trained as an assassination specialist by an unknown shinobi from a different village. This could lead to him having a double life, trying to balance his normal ninja duties in Konoha with his secret assassination missions. Another idea is that Naruto discovers a hidden group within Konoha that specializes in assassinations and has to decide whether to join them or expose them.
Perhaps Naruto becomes an assassination specialist after losing someone dear to him in a brutal way. He decides to use his skills to target the criminal underworld that caused the harm. He could start off on his own, but as his actions gain attention, some of his friends, like Shikamaru, might suspect what he's up to. Shikamaru could then either try to stop him or help him depending on the situation. Naruto would have to operate in the shadows, using his Uzumaki heritage and new -found stealth skills to take down his targets one by one.