Perhaps Sasuke is possessed by some extremely evil entity. And Kakashi, in an attempt to stop the entity from causing more destruction, decides to kill Sasuke. It could also be that Sasuke discovers some dark secret about Kakashi that Kakashi doesn't want revealed, and in a moment of panic and self - preservation, he kills Sasuke.
Well, it could be that Kakashi is under some sort of dark spell or curse that makes him see Naruto as a threat to the village. In some fanfictions, there might be a situation where the village's safety is at stake and Kakashi believes that sacrificing Naruto is the only way to save everyone. Also, it could be a case of false information. If someone convinces Kakashi that Naruto has turned evil and is about to cause great harm, he might take the drastic step.
Often, Gai is paired with Kakashi in Hurt Kakashi fanfiction. Gai, with his unwavering belief in friendship and his eternal rivalry with Kakashi, can be a great character to interact with a hurt Kakashi. He might try to pull Kakashi out of his slump through their friendly competition. Also, Rin is sometimes included. Since she has a significant past with Kakashi, her presence in the fanfiction can either be a source of comfort or more pain, depending on how the story is written.
In such fanfiction, the Kakashi OC often has unique physical features. For example, they might have distinct hair color or eye shape that sets them apart.
Kakashi might be initially surprised. But then, he would probably use it as a teaching moment for Naruto. He could say something like 'Naruto, stealing is not the way of a ninja.' And then give him a punishment like extra training.
Often, Naruto is paired with Kakashi in such fanfictions. Their bond from the original series can be explored in new ways in the context of Kakashi's reincarnation. For example, Naruto might be the one to discover Kakashi's reincarnated form and help him adjust.
Kakashi could use his Sharingan to analyze Obito's moves and find a weakness in his defenses. Since he has the Sharingan, he might be able to predict Obito's attacks and counter them effectively, eventually finding an opportunity to break free.