Perhaps in the fanfiction, Percy is forced into a situation where he has to choose between Thalia's life and the safety of many others. If the situation is presented in such a way that killing Thalia seems like the only option to save a large number of people, he might be pushed to do it. It could also be related to some prophecy that Percy misinterprets. If the prophecy seems to suggest that Thalia will bring great doom, and Percy takes it too literally, he could end up trying to kill her.
One possible motive could be self - defense. Maybe Ares was about to harm Percy's friends or family, and Percy had no other choice but to fight back and end up killing him.
One possible motive could be a misunderstanding. Maybe Hercules is framed for something really bad, and Percy, believing the false information, decides to take action. For example, if there's a plot where Hercules is made to seem like he's about to destroy a city full of innocent people, Percy might feel it's his duty to stop him, even if it means killing him.
One possible motive could be a misunderstanding. Maybe the Hunt has been misinterpreted as a threat to Percy's friends or Camp Half - Blood. So in his attempt to protect his own, he takes extreme action.
Perhaps Percy had lost someone very dear to him because of Tartarus. This could have filled him with so much rage and a thirst for revenge that he decided to kill Tartarus. In fanfics, emotions often drive characters to extreme actions. Percy, being a hero, might have thought that taking out Tartarus was the ultimate way to avenge the wrongs done to him and those he cared about.
One possible motive could be to protect his friends and the world. Typhon is a powerful and dangerous being. Percy might see that Typhon's existence poses a huge threat to everyone he cares about, like Annabeth, Grover, and all the other demigods. So, in order to safeguard them and the world from Typhon's potential destruction, he decides to kill Typhon.
It could also be about power. Percy might realize that with Zeus out of the way, he can reshape the world of the gods in a more just and fair way. He could believe that Zeus's rule is corrupt and that killing him is the only way to bring about real change.
One possible motive could be that Minato is under some sort of dark magic or mind control. In fanfiction, authors often play with the idea of characters being forced to act against their true nature. So, if Minato is being controlled, he might end up doing something as extreme as killing Naruto.
One possible motive could be that Harry is under the influence of a dark spell or curse that makes him lose control of his actions. In some fanfiction scenarios, dark magic can overpower a character's true nature.
One possible motive could be a misunderstanding. Maybe Haku was disguised as someone else who was about to attack Naruto or his friends, and Naruto reacted in self - defense without realizing it was Haku. Another could be that in this fanfiction, Naruto has been somehow corrupted or influenced by a dark force that made him lose his normal judgment and attack Haku.
It could be that his siblings have made a pact with an extremely evil entity. Naruto, with his sense of justice and loyalty to the greater good, decides that their existence in that state is too dangerous and kills them, though it would be a very difficult and heart - wrenching decision for him.