One possible motive could be jealousy. Hermione is highly intelligent and often outshines Draco in academics. In a twisted version of a rivalry, Draco's envy could turn into a deadly hatred. Another could be his family's influence. If the Malfoys push him to take extreme actions against Muggle - borns, Hermione would be a prime target.
Maybe in some fanfictions, Draco is driven by a sense of self - preservation. He might believe that Harry will eventually turn against him or the Slytherin house. He could think that by killing Harry, he can secure his own place at Hogwarts and in the wizarding community. Additionally, it could be part of a larger plot by Voldemort or his followers. If Draco is forced to join Voldemort's side, he may be given the task of killing Harry to prove his loyalty.
It could be a revenge plot gone too far. Suppose her parents did something in the past that she just found out about, and in her new dark persona, she decides to take the ultimate revenge. Or perhaps she has fallen so deep into the dark side that she no longer values family and sees them as just another obstacle in her path of darkness.
Another motive might be related to a dark object influencing her. If Hermione came across a cursed object, like a dark locket that amplified negative emotions such as envy or fear, it could drive her to kill Harry. Maybe she started to envy Harry's fame and the special attention he always got, and the locket pushed her over the edge.
Maybe it's out of envy. He sees Hermione's abilities and popularity and wants to possess her in a way. He might think that by forcing her to marry him, he can somehow be part of what she represents in the wizarding world.
One possible motive could be jealousy. If Kiba were to gain more recognition in the village than Naruto in the fanfiction world, Naruto's insecurities could drive him to do something drastic like killing Kiba. But this is a huge departure from his usual self.
Differing ideologies during the wizarding war. If James was seen as a threat to Snape's side (even if Snape was on the wrong side, from a moral perspective), Snape could justify killing him. For example, if James was too aggressive in fighting the Death Eaters and Snape thought it would lead to more bloodshed, he might take matters into his own hands to stop James.
One possible motive could be revenge. The Dursleys treated Harry awfully for years, so in fanfiction, he might reach a breaking point. Another could be self - defense if the Dursleys in the fanfiction were to take their abuse to an extreme level.
One possible motive could be self - preservation. Draco might realize that the Death Eaters are losing and that siding with the Order gives him a better chance of survival.
Jealousy could be a big motive. Harry is often the center of attention, and Draco, who is used to being in the spotlight in his own Slytherin circle, might be jealous. So he punishes Harry to try and knock him down a peg or two.
Perhaps Stiles discovers some dark secret about the alpha pack that endangers the entire town or the supernatural world he's a part of. In his sense of responsibility and his unique way of thinking, he figures that killing the alpha pack is the only solution to prevent a greater catastrophe. This can add a lot of depth to the fanfiction story, exploring Stiles' moral compass and his ability to make tough decisions.