It could end with Snape realizing he was wrong. He apologizes to Harry and they form an unlikely alliance. They return to Hogwarts together and Snape has to face the consequences of his actions from Dumbledore.
Maybe Harry manages to escape from Snape on his own. But instead of hating Snape, he understands that Snape was probably acting out of some strange reasoning. So, Harry decides not to report Snape and they keep their distance from each other.
Well, it could be that Snape has some false information that makes him think Harry is in immediate danger from the wrong people at Hogwarts. So, he kidnaps Harry to protect him. Maybe he takes Harry to a secret location like an old, abandoned wizarding house in the Forbidden Forest. There, he tries to figure out what to do next while Harry is really confused and angry at being kidnapped.
Well, Harry might discover some hidden passageways in Voldemort's lair. Since he has a lot of experience with tricky situations at Hogwarts, he could use his wits to find a way out. Also, he could try to appeal to any shred of humanity left in Voldemort's followers, if there are any, and get them to help him escape.
It could end with Lily escaping and being forever angry with Snape. She might cut all ties with him and go on to marry James Potter, with Snape left full of regret for his actions.
One possible plot could be that Harry is under the influence of a dark spell. In this state, he kidnaps Ginny because the spell is making him act against his true nature. Ginny, being the strong - willed character she is, tries to break through to Harry and reverse the spell's effect on him.
Perhaps the ending involves Hiccup actually being the key to saving Toothless from his own actions. Hiccup manages to communicate with Toothless on a deeper level, and they work together to defeat the real enemy that was causing Toothless to act out. In the end, their bond is stronger than ever, and they continue to protect Berk side by side.
Well, perhaps Snape has some desperate reason. Maybe he's trying to protect Lily from the Dark Lord in his own twisted way. He might think that by taking her away from the wizarding world for a while, he can keep her safe from Voldemort's reach.
Perhaps Fleur is being controlled or influenced by a dark force. In the Harry Potter universe, there are many dark magic entities that could manipulate someone into kidnapping Harry. It could be that she is under the Imperius Curse or some other form of mind control. Another reason could be that she has some sort of personal vendetta against Harry or those close to him, and kidnapping him is her way of getting revenge. She might think that Harry has wronged her in some way, whether it's real or just in her deluded perception.
In this fanfiction scenario, Snape might be under the influence of a dark spell or some form of blackmail. He kidnaps Harry as a result. However, Harry, being the resourceful character he is, might start to figure out Snape's true situation and try to help him break free from whatever is controlling him.
Often, it could end with Hermione being rescued. Maybe Harry and the others stage a big rescue mission and manage to defeat Voldemort in the process.
Perhaps in the fanfic, Snape discovers a powerful and dangerous magic that he wants to use for what he believes is the greater good, but Harry sees it as a threat. Harry has always been wary of Snape, and this new discovery could be the tipping point. Also, if Snape were to make a deal with a dark force in order to gain knowledge to defeat Voldemort but Harry misinterprets his intentions, it could lead to Harry killing Snape.