Maybe Sakura is sad because she feels she's not strong enough compared to her peers. Naruto then challenges her to a friendly spar. During the spar, he points out all her strengths and unique skills, like her precise chakra control. This makes Sakura feel better about herself and lifts her spirits.
One possible scenario could be that Sakura is feeling down because she failed a difficult medical ninjutsu exam. Naruto, being the good friend he is, takes her out for her favorite ramen and tells her stories of his own numerous failures and how he never gave up. This cheers her up as she realizes that failure is just a stepping stone to success.
In a scenario where Sakura is missing Sasuke and is feeling lonely, Naruto could bring her a small gift, like a flower he picked on his way. He then sits with her and shares his own experiences of missing people, and how he copes with it. His presence and words of comfort cheer Sakura up.
One possible scenario could be after Naruto loses a difficult battle. Hinata might find him sitting alone, looking dejected. She could sit beside him and start by saying how she saw his amazing efforts during the fight. Then she might share some of her own insecurities and how Naruto's determination has always inspired her. This would remind Naruto of his own importance and boost his spirits.
In some fanfictions, Naruto might punish Sakura for betraying their friendship. For example, he could distance himself from her, making her realize how her actions have hurt him.
One possible scenario could be Naruto being forced into a situation where he has to seem to betray Sakura to protect her from a greater danger. For example, he might be blackmailed by an enemy into staying away from her or acting against her interests.
One possible scenario could be that after a long and difficult battle, Sasuke realizes how much Sakura has always been there for him. In a moment of vulnerability and newfound appreciation, he leans in and kisses her. It's a kiss full of unspoken emotions and a new beginning for their relationship.
Well, perhaps in a fanfiction, Sasuke could cry for Sakura when he discovers a deep secret she has been hiding. Maybe it's something that makes him understand her on a whole new level, like a hidden pain she has endured all this time for his sake. This newfound understanding could stir such strong emotions in him that he can't hold back his tears.
One scenario could be when Sakura is being unfair in a team decision. Naruto would speak up and say that they need to consider everyone's opinion equally. He's not afraid to challenge her because he believes in fairness within the team.
One possible scenario could be in a great battle against an extremely powerful enemy. Maybe Naruto uses up all his chakra trying to protect the village from a huge threat like a new and terrifying Akatsuki-like organization. His body just gives out from the overexertion.
One possible scenario could be that all of Naruto's friends are killed in a great battle. He survives but is left alone, haunted by the memories of his lost comrades. He might then wander the world, a solitary figure, with his only company being the memories of the past.
Naruto's optimistic personality is a big factor. His ability to always see the bright side of things can rub off on Sakura. For example, if Sakura is worried about a mission, Naruto will be all like 'Don't worry, Sakura -chan! We've faced tougher things and we always come out on top!'. His positive outlook makes Sakura believe that things will be okay.
One way to write a cheering up scenario in a Naruto fanfiction is to have his friends come together. For example, Sasuke could return after a long time and they have a friendly spar. During the spar, they exchange words of mutual respect and understanding, which could cheer Naruto up as it shows the bond between them is still strong.