Perhaps a really unexpected plot twist could be that their time travel is not by accident. There is a powerful, unseen force that has sent them back in time. And this force has a specific mission for them. But as they start to fulfill this mission, they discover that the force has its own dark motives and they have to decide whether to continue or go against it. This adds a whole layer of mystery and moral dilemma to the fanfiction.
One interesting plot twist could be that when Merlin and Morgana time travel, they end up swapping their magical abilities. So Merlin has Morgana's dark magic skills and vice versa. This creates a whole new dynamic as they struggle to adapt to these new powers in a different time period.
A plot twist might be that the baby has some sort of prophetic power even before it's born. This power could show visions to Morgana or Merlin about the future of Camelot. It could also be that the pregnancy is part of a grander magical plan set in motion centuries ago by an ancient sorcerer, and Merlin and Morgana are just pawns in this plan, not realizing the true significance of the pregnancy until later events unfold.
A really cool plot twist in some 'Harry Potter and Morgana Merlin fanfiction' is the idea that Morgana was actually an experiment by an ancient wizard in the Harry Potter world long ago. So her presence in the Merlin universe was a sort of exile. When she returns to the Harry Potter world, she has a different perspective and new powers. Another interesting twist is that the sorting hat in Hogwarts is actually an artifact from Merlin's time, and it has a hidden connection to Morgana. This connection is revealed when a new student arrives who has a special link to both universes, and it sets off a chain of events that no one could have predicted.
The child could be a bridge between the two opposing sides that Merlin and Morgana represent. The child's innocence and unique perspective could start to change the views of those around them, leading to a possible reconciliation between Merlin's side and Morgana's followers. This would involve a lot of character development for the child as well as for Merlin and Morgana as they see the world through the eyes of their offspring.
Another plot could involve Merlin traveling to the future. He might see a desolate Camelot, destroyed by some unknown force. Then he has to return to his own time and figure out how to prevent this dark future from happening. This would involve him using his magic in new and creative ways to influence the present to change the future.
One plot idea could be Merlin reveals a long - hidden prophecy to Morgana that involves her true destiny. Another could be Merlin tells Morgana about a secret magical realm that only he knows of, and they embark on a journey to explore it. Or perhaps Merlin tells Morgana about his own insecurities and fears regarding his magic, which in turn makes Morgana open up about her own struggles.
One idea could be that Merlin teaches Morgana about the old magic in a secret grove. He shows her spells that can heal the land, and they bond over their shared connection to magic. Another could be Merlin teaching Morgana how to control her visions, which she's been struggling with. It could lead to a deeper understanding between them and a new alliance within Camelot.
One idea could be that their kiss is a moment of realization. Maybe they've been enemies or at odds for a long time, and the kiss makes them see each other in a new light. For example, Morgana realizes that Merlin's magic isn't as bad as she thought and that he has been trying to protect Camelot all along. Another plot could involve a magical bond that forms through the kiss. This bond could give them shared powers or make them telepathically linked, leading to some really interesting interactions as they learn to deal with this new connection. A third idea is that the kiss is a secret pact. They kiss to seal a deal to work together against a greater evil that threatens Camelot, but they have to keep their new alliance a secret from everyone else in the kingdom.
Perhaps the person who initiates the time travel isn't who they seem. It could be an imposter who has their own motives for changing the past, like a Shadow in disguise. This would add a whole new layer of mystery and danger to the story.
Merlin would likely become more cautious. In a time - travel situation, he'd know that his actions could have huge consequences for the future. For example, if he accidentally reveals too much about his magic in the past, it could change everything. Morgana, on the other hand, might see an opportunity for power. She could try to use her knowledge of the future to gain a stronger position in the past.
A plot that often shows up is the idea of soulmates. In fanfiction, Merlin and Morgana could be fated to be together as soulmates. Their love is written as something that is destined, and no matter how much the world tries to keep them apart, they keep being drawn back to each other. Another interesting plot is that Morgana has a premonition of their love and future together, and this changes her attitude towards Merlin from the start. She then tries to find ways to make their relationship work despite all the odds in Camelot. And there are also fanfictions where they meet in secret and have a secret relationship, with all the tension and excitement that comes with hiding their love from the people around them.