Perhaps Harry Potter travels back in time and ends up befriending a younger Bellatrix. He could try to influence her to not become a Death Eater. This would create a really complex situation because he has to balance not changing too much of the future while also trying to save her from the dark path. It could lead to some really intense moments where Harry has to hide his true identity and motives from her.
A possible plot twist could be that when they both travel back in time, they accidentally swap their magical powers. So Harry has Bellatrix's dark magic abilities and Bellatrix has Harry's more 'good' magic. This would force them to adapt to new ways of using magic and also change their relationships with other characters. For example, Bellatrix with Harry's powers might be seen as less of a threat by the Order of the Phoenix at first, while Harry with her powers might struggle to control the dark side of magic.
In some fanfics, a time - traveler might end up being the cause of Grindelwald's rise instead of stopping it. For example, in 'The Unintended Consequence', the main character's actions in the past accidentally give Grindelwald more power.
A plot twist could be that the Dementors in Azkaban are not what they seem. Harry and Bellatrix find out that they are being controlled by a greater, more sinister force. This discovery makes them put aside their differences and fight together against this new threat, which is something no one would expect considering their prior relationship.
One interesting plot twist could be that when Harry travels back in time, he accidentally alters the events that led to Andromeda's relationship with the Black family. This could create a whole new set of family dynamics for her. For example, if Harry stops her from making a certain choice, it might lead to her being more involved with the dark side of the wizarding world initially, but then his presence in that time could also be the catalyst for her to change again and become a key figure in fighting against the dark forces in a different way than in the original timeline.
One possible fanfiction could involve Bellatrix going back in time to try and change the outcome of the Battle of Hogwarts in her favor. Maybe she uses time - turners or some dark magic to travel back. She could attempt to kill Harry Potter as a baby before he even becomes a threat.
Perhaps Lucifer is actually an ancient dark wizard who was banished long ago and is now trying to return using the chaos of the wizarding war in Harry Potter's time. He could manipulate events from the shadows, and Harry, with the help of Dumbledore's portraits (which have some ethereal knowledge), figures out Lucifer's true identity and purpose, leading to a showdown that combines magic from both universes.
One interesting plot twist could be the seer seeing a future where Voldemort is actually a puppet of a more powerful dark wizard hidden in the shadows. This would completely change the power dynamics in the wizarding world.
They could time travel to a future where everything they knew is in ruins. In this desolate future, they find out that their actions in the past led to this destruction. Now they have to work together to go back in time again and correct their mistakes. Sakura uses her intelligence to figure out what went wrong, while Madara uses his combat skills to protect them during their journey through time.
A really cool plot twist would be if during their time travel, they find out that time itself is a sentient being or is being controlled by an unknown force. This force has been manipulating events in the Soul Society and the human world all along. Ichigo and Urahara then have to figure out how to deal with this new discovery, whether to fight it or try to negotiate, while also trying to find their way back to their own time.
She could travel back to the time when Voldemort was still in hiding as a young Tom Riddle. Bellatrix might try to influence him in a different way, perhaps making him even more ruthless. This would change the course of the wizarding world in a very different direction.
One interesting plot twist could be Naruto changing the past in a way that completely alters the future relationships. For example, if he manages to prevent certain tragedies from happening to his friends' families, it could lead to very different dynamics. Maybe Sasuke's family wouldn't be massacred, and Sasuke would grow up in a completely different environment, which might change his entire attitude towards the village and Naruto himself. This could lead to a whole new set of adventures and challenges for Naruto as he tries to adapt to this new timeline.