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.
In the 'Jotaro meets McCree fanfiction', a really unexpected plot twist could be that McCree's past is somehow connected to an ancient Japanese mystery that Jotaro has been investigating. This would make their meeting not just a chance encounter but something fated. Or, they could discover that the powers they thought were unique to their own worlds are actually related at a deeper level. For instance, the energy that powers Star Platinum might be the same as the strange energy that McCree has noticed in some of the artifacts in his world. This realization would change their entire approach to dealing with the threats in the fanfiction.
Well, they might have an epic showdown at first. Jotaro with his Star Platinum and McCree with his Peacekeeper. But then they could realize they have a common enemy and team up. Maybe they'd exchange stories about their different worlds.
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.
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.
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.
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.
A plot twist might be that Videl is actually related to one of Gohan's enemies in some way. This would create a huge conflict between them. Also, it could be that there is a prophecy about Gohan and Videl that they are not aware of, and when they find out, it completely changes their relationship. Maybe Gohan loses his powers temporarily, and Videl has to protect him, which is a role reversal from what is expected in the DBZ world.
A possible plot twist could be that Vegeta Jr is actually an imposter sent to deceive Vegeta. He could initially seem like a legitimate Saiyan but gradually reveal his true motives, which might be related to an enemy's plan to take down Vegeta.