In the fanfiction, the main antagonist could be a dark and ancient force that has awakened. Sakura fakes her death to get closer to this force without it suspecting her. She then tries to find a way to defeat it, while the force believes it has eliminated one of its potential threats.
Perhaps in the fanfiction, Sakura fakes her death as part of a plan to deceive a rival ninja group. She might want to make them think they have won, and then when they let their guard down, she can strike back with a surprise attack. This could also involve her using a new, secret jutsu she has been developing.
It could be an envious noble. This noble might be jealous of Sakura's position as a princess and her popularity among the people. So, they try to spread false rumors about her and plot to dethrone her.
It could be Orochimaru. Even though he's had his moments of redemption, he might relapse into his old ways. He could see Naruto's 'death' as an opportunity to carry out some evil plan that Naruto would have stopped. Maybe he wants to use Naruto's death to create chaos and then take advantage of the power vacuum in the ninja world.
Maybe it's a rival within the mafia. Someone who sees Sakura as a threat to their own position or power. This person could constantly try to undermine her and make her life in the mafia even more difficult, even if the mafia boss doesn't have any ill intentions towards her at first.
One interesting fanfiction could be where Sakura Haruno somehow gets her hands on the Death Note. Maybe she uses her ninja skills to keep it hidden from the Shinobi world while trying to figure out how to use it without getting caught by Light or the Shinigami. Another could be a crossover where the Death Note world's rules are introduced to the Naruto universe and Sakura has to deal with the moral implications.
The crossover aspect is also very popular. Writers like to imagine how the characters from Naruto and Death Note would interact. For instance, how would Sakura react to Ryuk? Would she be scared or intrigued? And how would Light view Sakura's abilities? These interactions between the two very different universes are often the focus of many fanfictions.
The plot might involve Sakura being in a moral dilemma. Since she's a healer in the Naruto world, using the Death Note which is a tool for killing would go against her nature. So, it could be about how she struggles with this new power that she has and tries to find a way to use it without sacrificing her values.
She might become more confident, or overconfident. Having the Death Note gives her a huge advantage over her enemies. She could start to rely too much on this power and think she can solve all problems with it. This could lead to her making mistakes and alienating her friends.
I don't know for sure, but since it's a fanfiction centered around Sakura Haruno, she is the main focus. However, it may also feature characters who had a major impact on her life. This could include her sensei, like Tsunade, who trained her in medical ninjutsu. There's also a possibility that new characters created specifically for this fanfiction could be main characters as well, but that's just speculation.
In some Sakura Haruno alpha fanfiction, Kakashi could be a significant character. He might act as a mentor to Sakura in her new alpha role. He could guide her in making difficult decisions, like when she has to choose between the safety of the village and the life of a comrade.