Maybe it's a case of misinformation. In the chaos of the Wave arc, Sasuke could have been tricked into believing that Sakura is a threat. He might have received false information that she is working against him or Konoha, and in his haste and over - confidence, he kills her without fully understanding the truth.
Another reason could be related to the emotional turmoil Sasuke is in. He has lost his family and is constantly struggling with feelings of revenge. Sakura might have said or done something during the Wave arc in this fanfiction that triggers his dark side. For example, if she tries to make him abandon his quest for revenge against Itachi, he could lash out in anger and end up killing her.
One possible motive could be that Sasuke has been consumed by his thirst for power. In the Naruto universe, Sasuke has often been shown to be willing to sacrifice a lot for power. In this fanfiction set in the Wave arc, perhaps he sees Sakura as an obstacle to his pursuit of power, either because she tries to stop him from following a dark path or he believes she will hold him back in some way.
One possible motive could be that Sakura is brainwashed. Maybe an enemy uses some kind of mind - control jutsu on her and she becomes a puppet to kill Sasuke. Another could be extreme jealousy. If she felt that Sasuke was slipping away from her in some way, in a very dark and twisted version of the story, it could lead to her killing him.
A possible motive could be a creative exploration of the 'what - if' scenarios. Maybe the writer wants to see how the story would unfold if Sasuke completely lost his way. Another motive could be to create a sense of high - stakes drama. Since Sakura is an important character, her death at Sasuke's hands would be a huge shock.
One possible motive could be if Sasuke goes too far in his pursuit of power and becomes a threat to the entire ninja world that even Naruto can't reason with. Maybe Sasuke starts to kill innocent people without hesitation, and Naruto, as the protector of the village and the one who believes in peace, sees no other option but to stop him by killing. Another motive could be some kind of dark magic or mind control that makes Sasuke an uncontrollable force of destruction, forcing Naruto to take drastic measures.
One possible motive could be extreme jealousy. Maybe in this fanfiction, Hinata is insanely jealous of Sakura's relationship with Naruto or her skills, and that drives her to the unthinkable act of killing.
One possible motive could be self - preservation. Maybe he sees using Sakura as a means to create a distraction so that he can get away from a dangerous situation or from someone who is after him. He might think that her feelings for him make her an easy target to manipulate in order to achieve his goal of escape.
One possible motive could be some sort of mind control. Maybe a powerful enemy has the ability to control Percy's actions and forces him to go after Artemis. This would add an element of tragedy as Percy would be acting against his will.
One possible motive could be a dark magic or mind - control situation. Maybe an enemy has the power to control Naruto's actions and forces him to kill Sasuke against his will. Another could be a miscommunication where Naruto believes Sasuke has done something unforgivable, like harming the village in a way that Naruto can't overlook.
Perhaps in a fanfiction where the world has been completely turned upside down. If Sasuke had been tricked into becoming an unstoppable villain who was about to destroy the entire ninja world, and Sakura was somehow aiding him (maybe under a genjutsu), Naruto might feel he had no choice but to stop them by killing. Another reason could be a broken heart. If Naruto loved Sakura deeply but she constantly rejected him and chose Sasuke, and then Sasuke and Sakura betrayed him in some way, his anger and pain could lead to such a drastic act.
One possible motive could be revenge. Bellatrix killed Sirius, who was very dear to Harry. So in the fanfiction, Harry might be driven by the intense desire to avenge Sirius' death.
One possible reason could be that Sasuke was under some kind of mind - control or dark influence at that moment. Maybe he was influenced by an enemy's jutsu that made him lose his sense of self and turn on Sakura.