One plot twist might be that the source of Natsu's time - becoming ability is actually a dark force. He initially thinks it's a great power, but as the story progresses, he discovers that it's slowly corrupting him or has some hidden and dangerous agenda. This could lead to an internal struggle within Natsu as he tries to either control or get rid of this power. Another twist could be that time - based changes Natsu makes end up creating an alternate reality that he has to fix before it's too late.
One possible plot twist could be that when they time travel, they accidentally change a key event in the past that has a domino effect on their present. For example, they might prevent the formation of a guild that was crucial in their original timeline. Another could be that they find out they are related in some unexpected way through their time - traveling adventures. Maybe Ultear discovers she has a connection to Natsu's family that was lost in history. Or perhaps they time travel to a future where everything they know is in ruins, and they have to figure out how to prevent it in their present.
Another plot twist could be that the past they remember isn't actually real. It was all an illusion created by a powerful mage. When they find out, they have to figure out who the real enemy is and why they were put in this false past. This would completely shift the focus of the fanfiction from their relationship in the 'past' to finding out the truth behind the illusion.
One possible plot twist could be that Zeref actually doesn't want to fight Natsu seriously and has some hidden agenda. Another could be that Natsu discovers a new power during the fight that is related to his past or his true identity.
Well, one possible plot twist could be that Natsu has been hiding her true gender to be able to participate in male - dominated activities like a certain guild or sport. Another could be that she's in love with a male character, but is afraid to reveal her gender in case it changes how he feels. Or perhaps she has a special power that is related to her being a girl secretly, like a unique form of magic that only female dragonslayers can possess.
One common plot twist could be that as a female Natsu, she discovers new magical abilities that male Natsu didn't have. For example, she might be able to control certain elements in a different way. Another plot twist could be in the relationships. Maybe she has a different kind of bond with Gray. Instead of the competitive male - male relationship, it could turn into a more complex, perhaps even a romantic tension. Also, she could face challenges within the Fairy Tail guild that are specific to being a female in a male - dominated world of mages. The guild members might have different expectations of her, and she has to break through those stereotypes to prove herself.
One interesting plot twist could be that when Natsu turns into a dragon, he loses his memory of his human friends. This would create a lot of drama as his friends try to bring back the Natsu they know. Another could be that he turns into a different kind of dragon than expected, perhaps one with a very rare and powerful ability that attracts the wrong kind of attention from dark forces in the fanfiction world. And also, he might transform into a dragon at a crucial moment during a battle, not only surprising his enemies but also his allies, changing the whole dynamic of the fight.
One possible plot twist could be that Natsu initially doesn't believe it's his child. Maybe he has some self - doubts due to his past or his own insecurities. Another twist could be that there are external forces trying to harm Lucy because of her pregnancy, like dark guilds seeing it as a way to get to Natsu. And perhaps the pregnancy could also bring out a new side of Natsu, a more protective and responsible side that no one has seen before.
A possible plot twist could be that one member of Team Hebi, say Karin, is actually from the future and has been manipulating the time - travel events all along to achieve a certain goal, like saving her own clan. This would completely change the team's dynamic and their perception of her.
One possible plot twist could be that Ichigo travels back in time and accidentally changes something that makes him not become a Soul Reaper in the first place. This would completely change his destiny and the future of the Soul Society. Another could be that he travels to a time when an ancient evil was first sealed away, and his presence there somehow weakens the seal, leading to a new threat emerging in his present time.
One possible plot twist could be that Ragna discovers he is the cause of a major historical event that he previously thought was just a part of history. For example, he might find out that his actions in the past led to the rise or fall of a powerful kingdom.