It could be a rogue ninja who was once a part of a secret organization. This ninja has a kekkei genkai that is the opposite of Sakura's and wants to destroy her to prove the superiority of his own power. He constantly hunts Sakura down and tries to ambush her during her missions.
Perhaps an ancient evil spirit that has been awakened due to some dark rituals. The spirit is envious of Sakura's newfound power and sees her as a threat to its plans of ruling the world. It uses its dark magic to corrupt other ninjas and turn them against Sakura, creating a difficult situation for her.
There could be a group of power - hungry shinobi from a neighboring village. They see Sakura's powerful kekkei genkai as a weapon that could give their village an edge. So they send their best assassins to either capture Sakura and force her to work for them or kill her to prevent her from becoming too powerful and a threat to their village.
Maybe her kekkei genkai gives her the ability to control time on a small scale. She uses this power to anticipate her opponents' moves in battles. In a fight against a powerful enemy, she freezes time briefly to analyze the situation and come up with a perfect strategy, which ultimately leads to her victory and earns her great respect among the shinobi community.
There's also the possibility that the main antagonist is a group of ninja from a rival village. They fear Naruto's new power and form an alliance to take him down. They might have spies within Naruto's village trying to gather information about his kekkei genkai so they can develop counter - measures and ultimately defeat him.
Well, it could be something like a fire - based kekkei genkai that allows Naruto to control blue - flame fire which is hotter than normal fire. This would give him an edge in battles and also a new look to his fighting style.
Perhaps her kekkei genkai is related to some form of elemental control that no one in Konoha has seen before. This could lead to a plot where other villages become interested in her power, either wanting to steal it or recruit her. Sakura then has to deal with the political and dangerous implications of having such a unique kekkei genkai while also trying to protect her village and friends.
I'm not sure of a specific fanfiction titled exactly like that off the top of my head. But you could try searching on fanfiction websites like FanFiction.net or Archive of Our Own. Just type in 'Sakura has a kekkei genkai' in their search bars and you might find some interesting stories.
In a fanfiction, Sakura's Kekkei Genkai could be related to some sort of mind - control or illusion ability. Since she's already intelligent, this power could enhance her skills in interrogation and strategic planning. She could use it to outwit enemies during battles, creating illusions that seem so real that opponents are left confused and vulnerable.
In Akatsuki fanfiction, Sakura Haruno might be given a unique Kekkei Genkai. It could be something related to enhanced strength or perhaps a special type of medical ninjutsu on a whole new level. For example, her Kekkei Genkai could allow her to heal not just physical wounds but also mental traumas instantaneously, which would be a very interesting addition to her character in the context of Akatsuki fanfiction.
It could be a rogue ninja from another village who is jealous of Naruto's new power. This ninja wants to steal the Kekkei Tota for himself and uses all kinds of underhanded tactics to try and get it from Naruto.
In some fanfictions, a side character from the original Naruto series could be made into the main character. For example, Rock Lee. He doesn't have any Kekkei Genkai in the original, but in this fanfiction, he could be given one of the 9 Kekkei Genkai and the story could be about how he overcomes the limitations he had before with his newfound power.
Well, in some fanfictions, Naruto might obtain all kekkei genkai through some sort of ancient and powerful jutsu. Maybe he discovers a hidden scroll or meets a mysterious sage who imparts this power to him.