One interesting plot twist could be Sakura having to adapt to Fairy Tail's magic system. Maybe she discovers a new form of her own chakra-based abilities that interact with Fairy Tail magic in unexpected ways. For example, her healing jutsu could combine with Fairy Tail's healing magic to create a super - healing spell.
Perhaps Sakura teams up with a Fairy Tail character who has a really different personality from her, like Natsu. Their clashing personalities could cause all sorts of chaos at first, but then they gradually learn from each other. This change in their relationship would be a significant plot twist, especially when they end up using their combined skills to defeat a powerful enemy.
Well, perhaps a great plot twist is that Naruto's immortality is actually a curse in the Fairy Tail universe. The magic there has a different set of rules, and his inability to die disrupts the natural balance. This could lead to him being hunted not just by villains but also by some of the more morally strict magic guilds. Also, imagine if Naruto discovers that his past enemies in the Naruto world are somehow connected to an ancient evil in the Fairy Tail world, and he has to fight them again in this new context.
One interesting plot twist could be when the magic from Fairy Tail interacts with the sins' powers in Nanatsu no Taizai. For example, if Natsu's fire magic somehow combines with Meliodas' full counter, creating a new and unexpected power. Another could be the characters being transported to the opposite universe and having to adapt. Like Lucy ending up in Britannia and having to deal with the Holy Knights while the Seven Deadly Sins end up in Fiore and face off against the dark guilds.
One interesting plot twist could be that characters from Fairy Tail end up in the world of Legend of Zelda and they discover that their magic has a completely different effect. For example, Natsu's fire magic might interact with the magical elements in Zelda's world in a way that either helps or hinders their quest. Another could be that the Triforce has an unexpected reaction to the Fairy Tail mages' presence, perhaps granting them new powers or cursing them. A third plot twist might be that a major villain from Legend of Zelda teams up with a dark guild from Fairy Tail to take over both worlds.
Sakura could fit in as a healer. In Fairy Tail, having a powerful healer is always valuable. Her medical ninjutsu skills would be highly regarded, and she could quickly become an important member of the guild when it comes to treating injuries after battles.
Another plot twist might be that the villains in the Fairy Tail world are the ones who summoned Godzilla, but they lose control of it. Now the Fairy Tail guild has to figure out a way to stop Godzilla while also dealing with the villains who caused the mess in the first place. It adds a layer of complexity to the story.
Well, a great plot twist might be that the characters from Fairy Tail end up in the world of Fullmetal Alchemist and are mistaken for some sort of alchemical creations. They then have to prove that they are not and in the process, they discover that their magic has some strange effects on the alchemy in that world. For example, Gray's ice magic could freeze alchemical reactions in unexpected ways. Another plot twist could be that the Gate in Fullmetal Alchemist has a link to the Fairy Tail's Celestial Spirit World. So when someone tries to open the Gate, they accidentally open a portal to the Celestial Spirit World instead, and all kinds of chaos ensues as spirits and alchemists meet for the first time.
One idea could be that Sakura somehow gets transported to the Fairy Tail world. She could use her medical ninjutsu skills to heal the wizards in Fairy Tail, which would be a new and useful ability in that world. Maybe she teams up with Lucy and they go on adventures together, with Sakura providing combat support and healing when needed.
A great plot twist could be that Alice is actually a long - lost Fairy Tail mage. Maybe she was sent to Wonderland as a child and lost her memories. Another one is that the Queen of Hearts in Wonderland is being controlled by a dark mage from Fairy Tail's world. It would turn the whole story on its head.
A great plot twist would be if the Fairy Tail guild members were transported to the Naruto world and had to adapt to ninja life. Or perhaps a character from Naruto, like Sasuke, gets corrupted by the dark magic in the Fairy Tail world. It would create a whole new dynamic as the other characters try to save him. Also, what if there was a prophecy in both worlds that the only way to save them was for a Fairy Tail wizard and a Naruto ninja to sacrifice themselves? That would be a very intense plot twist.
One interesting plot twist could be that some of the zombies are actually under the control of an old enemy of Fairy Tail who has resurfaced during the apocalypse. Maybe this enemy has found a way to use the zombie hordes to target Fairy Tail specifically.