The sense of isolation could be a motive. If Naruto never truly felt accepted in Konoha despite his efforts, he might snap. He's always wanted to be recognized, but if that never fully happens, he could turn on the village. For example, if he's constantly passed over for important missions or not given the respect he thinks he deserves as a powerful ninja.
Power could be a motive. She might want to have control over the vampire world or the humans in Forks. So she starts doing villainous things to gain that power.
Power hunger could be a motive. Tony already has a lot of power with his technology, but if he becomes obsessed with having more and more, it could lead him to evil. He might start to see others as obstacles to his power gain.
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.
Another possible motive is that Orochimaru sees Naruto as a potential powerful ally or tool. Naruto has shown great potential and growth throughout the series. Orochimaru could think that by taking Naruto and molding him in his own way, he could have a powerful weapon at his disposal. He might also want to use Naruto to get back at Konoha in some way, since Naruto is one of Konoha's most important assets.
Maybe in the fanfiction, Naruto is being controlled by some dark magic or a powerful enemy. This could force him to kidnap Lemon against his will.
Another motive might be jealousy. Suppose Naruto has something that the fem Kyuubi desires, like the love and respect of the people in the village. In that case, she could torture him out of envy, trying to make him lose those things that she covets so much.
One possible motive could be mind control. Maybe an enemy uses some kind of jutsu to make Naruto lose control and attack Sakura. Another could be a misunderstanding. For example, if Sakura was framed for something really bad, and Naruto in his hot - headedness believes it and attacks her. Or perhaps in a dark, alternate universe version of the Naruto world where the characters' personalities are twisted, Naruto might have a reason to attack her based on that altered personality.
One possible motive could be if Sasuke was on a path of destruction that endangered the entire ninja world. Naruto, as the protector of peace, might see killing Sasuke as the only way to stop him. For instance, if Sasuke was about to unleash a powerful and uncontrollable jutsu that would wipe out many innocent lives.
One possible motive could be a complete breakdown of the peace they had worked so hard to build. Maybe an outside force manipulates Gaara's mind, causing him to turn on Naruto. Another could be extreme jealousy over Naruto's popularity or power.
Maybe she's trying to protect Naruto from something she knows about but others don't. She might think that by kidnapping him, she can keep him safe from an imminent threat that the village or his friends are unaware of.