One popular plot twist could be a crossover of Percy Jackson characters with Unlimited Blade Works' magic system. For example, Percy discovers he can use magic in addition to his water powers. This would completely change the power dynamics in his battles and his relationships with other characters.
Another plot twist might be that the antagonists from Unlimited Blade Works somehow manage to enter the Percy Jackson universe and start causing chaos. They could target demigods, thinking they are a new source of power or a threat to their own plans. This would force Percy and his friends to team up in new and unexpected ways to fight this foreign threat.
Some characters from Unlimited Blade Works might have the ability to project their willpower or magic. In a fanfiction, they could teach demigods like Percy how to do this. So Percy could then use his demigod strength along with this new - found ability to overcome stronger enemies. For example, he could project his willpower to calm the seas during a storm rather than just using his water - controlling powers directly.
One popular plot twist is when they end up swapping powers. Percy suddenly has control over wind and lightning while Jason can control water. This flips the script and makes for some really interesting scenarios.
The 'Alternate Universe' trope is very much used. For example, an alternate universe where the events of Unlimited Blade Works and Highschool DxD are intertwined from the start. Maybe the Grail War is a regular occurrence in the Highschool DxD world. Another trope is 'Identity Reveal'. A character might be hiding their true identity from one universe while in the other, and when it's revealed, it causes a stir. Also, the 'Forbidden Love' trope can be interesting. If there are rules against a relationship between a character from Unlimited Blade Works and one from Highschool DxD, like a magical or social taboo, it can create a lot of drama and tension in the fanfiction.
One interesting plot twist is when Percy loses his powers temporarily. In this situation, Will and Annabeth have to step up in different ways. Will uses his medical knowledge and some newfound abilities related to his Apollo heritage to keep Percy alive, while Annabeth has to use her wits to figure out how to get Percy's powers back. This puts a strain on their relationships as they all adapt to the new situation.
Power-ups and new abilities are also a theme. Writers might give a character a new skill or a stronger version of their existing powers. For example, Shirou could discover a new way to project his weapons that gives him an edge in battle. And the theme of moral dilemmas often appears. Since the original work has complex moral issues, fanfiction can expand on these. Characters may face even tougher choices about using their powers and the consequences of their actions.
In the stories, the revelation about Luke being a traitor is a big plot twist. He was initially seen as a friend and mentor to Percy. But later, it turns out he has his own dark motives and is working against the gods, which adds a lot of complexity and danger to the story.
One interesting plot twist could be that Percy's water powers somehow interact with Elsa's ice powers in unexpected ways. Maybe when they meet, their powers combine to create a new form of frozen water element that has unique properties. Another could be that the demigods from Percy Jackson's world have to deal with the magical cold of Arendelle, which is a whole new kind of challenge compared to their usual Greek - related threats.
Perhaps a plot twist where the Mist from Percy Jackson's world starts to affect Tokyo Ghoul. The Mist could make humans in Tokyo see ghouls as something completely different, like mythical creatures from their own Japanese folklore. This would not only change how the humans in Tokyo Ghoul react to ghouls, but also how the ghouls themselves perceive their place in the world and their relationship with humans.
One interesting plot twist could be that Percy discovers a way to nullify Kratos' god - given powers. Maybe he finds an ancient artifact during the fight that has the ability to do so. Another could be that Kratos, instead of seeing Percy as an enemy, realizes they have a common goal against a greater evil in the fanfiction world and they end up teaming up.
In some fanfics, a plot twist could be that a demigod turns into a vampire. This completely changes the dynamic as they now have to deal with their new vampiric nature while still having their demigod powers. It's a really unique take on the crossover.