Perhaps they are in the middle of a new adventure when Emma realizes she's pregnant. This could add a whole new layer of tension as they not only have to deal with the external threats but also ensure the safety of the baby. They could seek help from their friends in Storybrooke, who have mixed reactions to the news.
One idea could be that they face challenges in their relationship while preparing for the baby. Maybe Hook is worried about being a good father because of his past. Another could be that Emma's magic has an unexpected reaction during her pregnancy, like protecting the baby in a magical way. And a third idea is that they discover a prophecy related to their unborn child which forces them to go on an adventure to protect their family.
In another scenario, both Captain Hook and Emma Swan are held for ransom by a new and powerful villain in their world. They have to work together, using their combined skills and the power of their relationship, to escape from captivity. This could involve Hook using his pirate wiles and Emma using her magic. They might also find unexpected allies along the way who help them in their quest to avoid paying the ransom and defeat the villain.
The relationship would likely become deeper. Hook would be more protective of Emma, always by her side. Emma might see a new side of Hook, a more tender and responsible side, which would make her fall more in love with him.
Well, a plot could revolve around Emma's pregnancy powers. Since she has magic, perhaps her pregnancy enhances it in unexpected ways. Hook could be both amazed and a bit worried as he tries to support her. They could also go on a journey to find a special midwife or healer who can understand the unique nature of Emma's pregnancy because of her magic.
A plot idea could be that Emma has prophetic dreams about the baby's future during her pregnancy. These dreams might show the baby having a great and important role in the magical world. Hook then becomes determined to make sure the baby can fulfill this role safely. Another idea is that a dark force tries to possess the unborn baby, and Hook and Emma have to find a way to prevent it, maybe by seeking help from Regina who has experience with dark magic.
Adventure is also a big theme. They are often on some sort of quest or journey together. For example, they might be searching for a magical artifact while also dealing with their feelings for each other. And there's also the theme of trust. Since they come from different sides, learning to trust each other is a crucial part of many fanfics.
One common theme is redemption. Captain Hook often has a past full of misdeeds, and in these fanfics, his relationship with Emma Swan can be a part of his journey towards redemption. For example, in many stories, he tries to change for her.
You can try fanfiction websites like Archive of Our Own (AO3). It has a large collection of fanfictions, and you're likely to find many about Captain Hook and Emma Swan having a baby there.
There are quite a few out there. In some fanfictions, like 'A New Beginning for the Hook - Swan Family', it delves into how their relationship evolves with the addition of a baby. It might show Hook being overly protective and Emma being the more practical one when it comes to raising their child. The story could also involve their friends from Storybrooke helping them out in different situations.
A plot could involve Emma having difficulties with her pregnancy due to her being the Savior and all the magic in her. Hook is overprotective and tries to find ways to ease her pain. Meanwhile, they learn that there are prophecies about their child that lead them on a journey to different realms to protect the baby's future.