A possible plot twist could be that the dragon is actually a shapeshifter and turns into a human form that Shirou knows. Maybe it's someone he thought was dead.
Well, a really interesting plot twist could be that the Crimson Dragon Emperor has a hidden connection to Shirou's past. Maybe it was involved in an event that shaped Shirou's life without him knowing. This would completely change the dynamic of the fight. Another plot twist could be that Shirou's power suddenly backfires during the fight, putting him in a dangerous situation where he has to rely on his wits rather than his magic. Or perhaps the fanfiction could introduce a time - travel element, where the fight is not really in the present but is part of a loop in time that they need to break.
A plot twist could be that Merlin is not who he seems. Maybe he has an ulterior motive for meeting Shirou, like using him as a pawn in a larger magical game. This would completely change the dynamic between them.
One possible plot twist could be that Kid Goku is actually from an alternate timeline and has some powers that Dragon Ball Z Goku doesn't expect. Another could be that a villain uses their meeting to his advantage, like creating a rift between them to cause chaos.
Well, a really interesting plot twist in 'Mario Meets Peach Fanfiction' could be that Mario himself is the one being tricked. Bowser has created a fake Peach to lure Mario into a trap. And while Mario is busy trying to rescue the fake Peach, the real Peach is actually in another location, in even greater danger. Also, there could be a plot twist where the power - ups that Mario usually relies on are actually cursed this time. When he uses them, they cause more harm than good. Maybe the super mushroom makes him too big to fit through the narrow passages he needs to reach Peach. Another possibility is that Peach has fallen in love with someone else in the time she has been captive, and Mario has to deal with this new emotional situation.
A possible plot twist could be that Videl turns out to have some hidden powers herself. It would completely change the dynamic between her and Gohan.
A plot twist might be that Jotaro loses his Stand abilities temporarily and McCree has to protect him. Or perhaps they find out that there's a traitor among the people they thought were their allies in this fanfiction world. This would force them to re - evaluate their situation and who they can trust. Also, it could be that a powerful artifact they were supposed to protect actually has the power to control them, and they have to fight against its influence.
One possible plot twist could be that Cersei pretends to surrender to Daenerys. Daenerys, believing her, takes Cersei into her confidence. But Cersei is actually plotting a big betrayal from within. She could be secretly gathering her remaining forces and planning to assassinate Daenerys when the time is right.
In the 'naruto meets nagato fanfiction', a plot twist might be that Nagato fakes his change of heart at first. He could be playing a long - game to deceive Naruto and the Leaf Village. Or perhaps, there is a prophecy that involves both of them, but it has been misinterpreted all along. And when they meet, they start to uncover the real meaning of the prophecy, which changes everything they thought they knew about their fates and the future of the ninja world.
One possible plot twist could be that Bowsette turns out to have some sort of connection to Naruto's world that he never expected. Maybe she has a hidden kekkei genkai - like ability that is related to Naruto's ninja powers.
One possible plot twist could be that the Dursleys are actually under a spell that makes them act so horribly, and Hermione discovers and breaks it. Another could be that Hermione finds out she has some family connection to the Dursleys, which would be a huge shock for everyone.