One idea could be a magical pregnancy. Maybe a powerful spell backfires on Yugi or Yami, and as a result, they end up in a situation where they are about to become parents. This could lead to a whole adventure of finding a way to reverse the spell while also dealing with the emotions and changes that come with the unexpected pregnancy.
One idea could be exploring how Yugi and Yami's relationship deepens during the pregnancy. Maybe they face challenges together like dealing with the reactions of their friends. Another could be the magical aspects of the mpreg in the context of their world, like how the pregnancy might be connected to the powers of the Millennium Items.
Maybe in a fanfiction, there is a prophecy that foretells of a child born from Hermione and Tom that will bring great change to the wizarding world. This prophecy forces them to be together, and they have to deal with the prejudices of others. Hermione uses her knowledge to try and understand Tom's dark past better, and Tom, in turn, learns from Hermione's kindness. The pregnancy then becomes a central part of the story as they wait for the birth of this prophesied child.
Perhaps in this fanfiction, Naruto and Korra find themselves in a situation where their pregnancies are part of a prophecy. They then have to figure out how to fulfill the prophecy while dealing with the normal challenges of pregnancy like mood swings and physical discomfort. They could meet other characters from their respective universes who help them on this journey, like Kakashi guiding Naruto on how to be a good father - to - be and Tenzin giving Korra advice on handling her new situation.
A possible plot could be that Yugi and Yami are under the influence of a love - inducing spell. They initially resist it but then give in to the feeling and kiss. Later, they have to figure out if their feelings are real or just because of the spell. Another idea is that Yami is about to be sent back to his own realm forever, and in a heart - wrenching goodbye, they share a kiss. And then there could be a plot where they are in a masquerade ball - like event in the Duel Monsters world, and not knowing each other's identities at first, they share a passionate kiss which then leads to a whole new exploration of their relationship when they find out who they really kissed.
One idea could be exploring how Yugi's friends react to the news. Some might be shocked, while others could be extremely supportive. Another could be the challenges Yugi faces during the pregnancy, like dealing with morning sickness and hormonal changes.
One plot idea could be that Naruto and Temari are forced into an arranged marriage for political reasons between their villages. Over time, they start to understand each other better and develop real feelings. Then, through some magical or medical miracle, Temari becomes pregnant. Another idea is that they go on a dangerous mission together, get separated from their teams, and during that time, they make a deep emotional connection which leads to Temari getting pregnant later on in a very natural and story - appropriate way.
Perhaps a story where a lemon is the key to unlocking a hidden part of Yugi's and Atem's past. Yami, being connected to both, helps in the journey of discovery. They might encounter old enemies and make new allies as they follow the trail left by the lemon.
The relationship can develop through mutual support during the pregnancy. Yami could be very protective of Yugi, always making sure he's comfortable and has everything he needs. Yugi, in turn, can rely on Yami and show his gratitude, which deepens their bond.
One plot idea could be that they discover the pregnancy during a time of great unrest in the village. Naruto and Fem Sasuke then have to work together to keep the news a secret while also trying to protect the village and their unborn child. Another could be that they struggle with how to tell their friends, especially those who might not approve of their relationship at first. They could face challenges like dealing with Sasuke's past enemies who might see this as an opportunity to target them.
A more romantic plot could be that Yami Yugi starts having strange dreams about Dark Magician Girl. In these dreams, they seem to have a deep connection. As he tries to figure out what these dreams mean, he starts to develop real feelings for her in the waking world. But there are many obstacles in their way, like the fact that she is a magical being from the Duel Monsters world.