One possible plotline could be Twilight Sparkle dealing with the physical and emotional changes of pregnancy while still having to fulfill her princess duties in Ponyville. Another could be her friends helping her prepare for the arrival of the new foal, like Pinkie Pie throwing a baby - themed party.
A plotline might involve Twilight Sparkle being transported to a Spartan - based realm. There, she has to prove herself in their combat trials. As she progresses, she discovers a conspiracy within the Spartan society that she has to expose using her intelligence and magic. Or perhaps she teams up with a group of Spartans to retrieve a powerful magical artifact that is of great importance to both her world and the Spartan world.
One possible plotline could be that Twilight Sparkle is kidnapped by a powerful dark magic user who wants to steal her knowledge of magic. Her friends then embark on a quest to rescue her, facing various challenges along the way. Another could be that she is kidnapped by an unknown force from another dimension for some sort of experiment. Her friends have to figure out how to cross dimensions to save her. A third plotline might be that a group of villains kidnap Twilight Sparkle to use her as a bargaining chip against Equestria, and her friends must find a way to outwit the villains and get her back safely.
One possible plotline could be that some sort of magical or scientific accident causes the two universes to collide. Sonic, while exploring the new world he has been thrown into, meets Twilight Sparkle. As they try to figure out how to get Sonic back to his world, they develop an unlikely bond that leads to a kiss. Another could be that an evil force is trying to take over both their worlds and they team up. During their adventures together, feelings develop and they end up kissing as a symbol of their new - found connection.
One plotline could be Goku finding Twilight Sparkle in a strange new world and taking her under his wing. He might train her in his fighting techniques, which could be really interesting as Twilight is used to magic - based solutions.
They often interact as teacher and student. Luna, with her vast knowledge of the old magic, can teach Twilight things that are not found in modern magic books. For example, Luna might show Twilight how to communicate with the spirits of the night.
One possible plotline could be that Twilight Sparkle is exposed to some dark magic that gradually corrupts her and turns her into a demon. As a demon, she might struggle with her newfound dark nature while her friends try to save her. For example, they could search for a way to reverse the transformation by looking for ancient spells or artifacts.
One possible plotline could be Twilight Sparkle having PTSD from a past battle or a traumatic event in Equestria. This might cause her to have nightmares and struggle with her magic. She could then go on a journey to overcome her PTSD, perhaps with the help of her friends.
One plotline could be about how Emily deals with the changes in her body and the new responsibilities. Maybe she has to adjust to the werewolf pack's protection of her even more. For example, they might be extra cautious about vampires now that she is pregnant.
I'm not sure of specific 'Princess Twilight Sparkle pregnant' fanfictions offhand. You could try searching on fanfiction platforms like FanFiction.net or Archive of Our Own. They have a vast collection of My Little Pony - related fanfictions and you might be able to find what you're looking for there.
Twilight Sparkle and Princess Luna often have interesting interactions in fanfiction. Fanfic writers might explore their relationship in different ways. For example, some might focus on their friendship, showing how they support each other in ruling Equestria or in magical studies. Others could create adventures where they team up against a common foe. There are also stories that delve into their individual growth and how they influence each other's development.