One idea could be that it's a magical pregnancy. Maybe Merlin was accidentally affected by a spell meant for someone else, and now he's pregnant with Gwen's baby in a very strange and magical way. This could lead to a lot of confusion and drama in Camelot as they try to figure out how to handle this unprecedented situation.
Another possibility is that it's a result of a wish gone wrong. Merlin and Gwen made a wish together, but it was twisted by some dark magic. Now Merlin is pregnant with her baby. This could be a story about how they work together to reverse the wish and deal with the emotions that come with the unexpected pregnancy, like shock, worry, but also a growing bond as they face this unique situation.
You could also develop the plot by focusing on the physical and emotional changes Merlin goes through during the pregnancy. He might struggle with the hormonal changes, just like any pregnant person would. Emotionally, he could become more protective of Gwen and the unborn baby. Meanwhile, they might have to deal with threats from outside forces who somehow find out about the pregnancy and want to use it for their own gain. This could add a lot of action and suspense to the fanfiction.
Perhaps Gwen discovers she has some latent magical ability during her pregnancy, which is awakened by the life growing inside her. This could cause a stir in Camelot as magic is feared. Merlin then has to step in to help Gwen control her powers and keep it a secret from those who would harm her. Also, Arthur could be faced with the dilemma of how to protect Gwen and the baby from the anti - magic sentiment in the court.
His magic would be crucial in safeguarding the baby. If there were any threats from dark magic, Merlin could sense them early on. He could then use his powers to counteract the dark magic, perhaps by creating a magical shield around the baby. Also, if the baby were to be born with some sort of magical ability (since Arthur and Gwen are in a magical world), Merlin could help the baby control and understand its powers as it grows up.
Merlin might become even more protective of Arthur. Since Gwen is carrying Arthur's child, Merlin would see it as his duty to safeguard the future of Camelot. He could be more involved in Arthur's personal affairs, which might initially annoy Arthur but eventually he'd come to appreciate Merlin's concern.
In a fanfiction, it could be that an evil sorcerer casts a spell on Gwen and Arthur's unborn baby. The baby starts to show strange and dangerous symptoms. Merlin is the only one who can sense what's really wrong. He has to race against time to break the spell. He delves deep into his magic knowledge and also consults ancient magical texts. Along the way, he has to hide his actions from those in Camelot who still distrust magic, all while trying to save the baby and ensure the future of Camelot's royal family.
Gwen would likely become more determined and strong - willed. Merlin's sacrifice would be a huge emotional blow to her. It might make her more resolute in fighting for the good he believed in, perhaps becoming a more fearless leader in Camelot. She may also carry a sense of guilt and a need to prove that his sacrifice was not in vain.
One idea could be that they discover the pregnancy unexpectedly. Maybe they were on an adventure and Gwen starts feeling unwell. They then go to a healer or use some alien tech to confirm the pregnancy. This could lead to a whole new set of adventures as they try to prepare for the baby while still dealing with their usual foes.
One plot idea could be that they initially struggle with the news. Maybe they're not fully prepared for it, and they have to deal with the reactions of their friends and family. For example, their friends might be shocked or have mixed feelings.
One great Merlin and Gwen fanfiction is 'A Royal Bond'. It beautifully explores their relationship in a world filled with magic and political intrigue. The author does a wonderful job of portraying Gwen's strength and Merlin's loyalty.
One of the interesting aspects of their friendship in fanfiction is how they influence each other's growth. Merlin's knowledge of magic and his adventures often expose Gwen to a world beyond her ordinary life. Gwen's kindness and strong moral compass also guide Merlin, especially when he is faced with difficult decisions regarding his use of magic.