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 there has been a series of events that led Percy to believe that the Hunt has become corrupted. If members of the Hunt start to engage in actions that go against the values Percy holds dear, like harming innocent demigods or getting involved in some sort of dark magic. Percy, being a defender of the good, might feel the need to step in and 'kill' the Hunt in the context of the fanfic to stop this corruption from spreading.
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.
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.
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 a sense of betrayal. If the gods had broken promises to Percy or his friends too many times, he might feel pushed to the edge. For example, if they failed to protect his loved ones despite his loyalty and service to them in previous adventures.
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.
The morale among the demigods would be greatly affected. The Hunt is often seen as a symbol of strength and unity for female demigods. If Percy kills them, it might create a divide between male and female demigods, leading to internal conflicts within the demigod community. Also, it would change the way demigods view Percy. Some might see him as a hero for eliminating a potential threat, while others would see him as a murderer for killing the Hunt.
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 plot could be that the entire Greek pantheon is thrown into chaos. Percy might be seen as a huge threat, and other gods and goddesses would either try to hunt him down or form alliances with him out of fear or a desire for power. Demigods would be forced to take sides, leading to massive battles among them.