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Tear Jerker: Naruto The Movie Road To Ninja
Sakura essentially telling Naruto that she wished Sasuke was around instead of him. It hadn't been a good day for Naruto up until then, as he had started to feel the full weight of not having his parents around. Then Sakura dragged him away just to complain about her's (which you could tell was starting to actually make him angry) and then she hit him with that. Keep in mind that Naruto has pretty much gone through hell just to get Sasuke back for her and himself so that comment was extremely harsh. Had Tobi not shown up immediately after to kickstart the actual plot of the movie and take their minds immediately off of that, the two's friendship likely would've been irreparably damaged.
Even better, Naruto made the choice for her. He really didn't want to leave but knew this world was not his own and he and Sakura still had family back in his main one.
Really, just the concept that AU!Naruto having two living parents with whom he lives a happy, normal life is what makes his life so bizarrely different from the real Naruto's. One scene has Naruto finding himself eagerly running home because he realizes that, for once, someone will be there to welcome him. He returns home to find his parents getting ready for dinner and happily greeting him. What would be a mundane event for most people almost brings Naruto to tears, because this will never happen in his actual life.
Naruto and Sakura starting to leave the alternate world and Naruto saying good bye for the final time to Kushina and Minato.