One possible plot twist could be that Tom Riddle kidnaps Harry not for the typical reasons like revenge or to gain power over the wizarding world. Maybe he discovers that Harry has some hidden knowledge about a long - lost magic that he wants for himself. Another twist could be that while kidnapped, Harry manages to find a way to get into Tom Riddle's mind and discovers his deepest fears, which he then uses to his advantage to try and escape. It could also be that there are other dark forces at play that Tom Riddle is actually trying to protect Harry from, in his own twisted way, by taking him away from the wizarding world for a while.
A plot twist could be that Tom Riddle kidnaps Harry with the intention of using him as a sacrifice, but during the process, he realizes that Harry has a unique magic within him that could potentially change the dark path he is on. This realization could cause internal conflict within Tom Riddle. Another possibility is that Harry's friends, instead of directly rescuing him, end up getting caught in a trap set by Tom Riddle as well. And then, they all have to work together to escape, which changes the dynamic between Harry, his friends, and Tom Riddle completely.
One possible plot twist could be that Tom Riddle discovers Harry has a hidden power that he didn't expect. Maybe Harry has the ability to resist Riddle's mind - control spells in a unique way. This could lead to a battle of wills between them where Harry tries to outwit Riddle while being held captive.
Harry would probably be very defiant at first. He has faced Voldemort (Tom Riddle) before and he won't go down without a fight. He would likely try to use his magic skills to escape or at least hold Tom Riddle off until he can find a way out.
One possible plot could be that Tom Riddle, using his charm and manipulation skills, lures Ginny into a secluded place under false pretenses and then takes her captive. He might be after some information that he believes Ginny has, perhaps related to the secrets of Hogwarts or the Weasley family. Ginny, being a brave character, would constantly try to resist and find a way to escape while Tom Riddle would be using his dark magic to keep her in check.
One possible plot twist could be that Sirius Black has a noble reason for 'kidnapping' Harry. Maybe he discovers a plot against Harry within Hogwarts that the school's authorities are ignoring. So, he takes Harry away to protect him. For example, he might find out that a certain teacher is under the influence of Voldemort and plans to harm Harry. Another twist could be that Sirius Black is being controlled by a dark magic spell and doesn't really mean to harm Harry. It could be a setup by Voldemort's followers to make Sirius look bad. Also, it could turn out that the 'kidnapping' is part of a secret training plan for Harry. Sirius wants to train Harry in some special magic skills away from the prying eyes of Hogwarts.
In certain fanfictions, a really interesting plot twist is when Harry Potter is sent back in time and ends up influencing Tom Riddle's early life in ways he didn't anticipate. This can lead to a completely different Hogwarts and wizarding world. For example, Harry might accidentally introduce a new form of magic that Tom then misuses. Or, there could be a plot twist where Tom Riddle's Horcruxes have an entirely different origin or purpose than in the original books, which throws Harry's understanding of how to defeat him into chaos.
One possible plot twist could be that Tom Riddle's dark tendencies start to resurface despite Hermione's positive influence. Maybe he begins to secretly manipulate those around him at Hogwarts while still maintaining a facade of being a reformed child. This could lead to a rift between Hermione and some of her friends who suspect Tom but don't understand why Hermione is so trusting.
One plot twist could be that the time travel is not accidental. In a fanfic I read, Dumbledore sent Harry back in time on purpose to try and redeem Tom Riddle. This changes the whole perspective of the story as it shows Dumbledore's more proactive and perhaps riskier side in dealing with the threat of Voldemort.
Harry would likely be defiant. He has faced Voldemort (Tom Riddle) before and he's not one to cower easily. So, he'd probably start looking for ways to escape right away, using his wits and any small magical items he might have on him.
Well, perhaps the plot could involve Hermione actually getting through to Tom Riddle in some way. Since she's so intelligent and empathetic, she might start to make him question his dark ways while being kidnapped. This could lead to a really interesting internal struggle within Tom. Also, there could be a twist where the kidnapping is part of a much larger plan that involves other dark wizards or witches, and Hermione has to figure out how to not only escape but also stop this bigger conspiracy. Or it could be that Hermione discovers a secret about Tom Riddle's past during her captivity that she can use to her advantage.
In some fanfictions, Bellatrix might kidnap Harry with the intention of turning him to the dark side. She could try to corrupt him by showing him the power and 'glory' of the dark magic she practices. This would be a huge psychological battle for Harry as he has always been firmly against the dark arts.