Maybe Twilight Sparkle is kidnapped by a time - traveling villain who plans to change the past in a way that would eliminate Twilight and her influence on Equestria. Her friends notice the sudden changes in the timeline and figure out that Twilight is missing from the altered history. So they have to time - travel as well to stop the villain and rescue Twilight. Another idea is that she's kidnapped by a group of magical creatures who are misinformed about Twilight and think she's a threat to their existence. Her friends would need to communicate with these creatures and clear up the misunderstanding while also rescuing Twilight.
Well, in some fanfictions, Twilight Sparkle could be kidnapped by a cult that worships an ancient and evil power. They think Twilight's connection to magic can help them awaken this power. Her friends would then need to infiltrate the cult's lair, which could be full of traps and other minions. Or perhaps she's kidnapped by a jealous rival from a different school of magic. This rival believes that by getting Twilight out of the picture, they can become the most powerful mage. In that case, Twilight's friends would have to prove her innocence and find her before it's too late.
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.
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 common plotline could be that Twilight's friends set out on a grand adventure to rescue her. They might face various obstacles and villains along the way. For example, they could encounter a powerful dark magic user who has kidnapped Twilight for her knowledge of magic. Another plotline might involve Twilight using her own wits and magic, even while kidnapped, to try and escape or send messages to her friends. It could also be that the kidnapper has some sort of vendetta against Twilight because of her status in Equestria and plans to use her as a bargaining chip.
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.
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.
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 interesting plotline could be Twilight Sparkle struggling to adapt to the changeling society while still holding onto her own values. For example, she might have to learn their ways of communication which are different from ponies.
It could be Discord. He loves causing chaos and kidnapping Twilight Sparkle would be a great way to disrupt the harmony in Equestria. He might do it just for fun or to see how Twilight's friends would react.
Well, in this type of fanfiction, it might be that Twilight Sparkle is betrayed by a mentor figure. This mentor could have been teaching her false information all along, causing her to make mistakes that put her and her friends in danger. Or it could be that she is betrayed in a love - related situation. For example, if she has feelings for a certain pony and that pony pretends to reciprocate only to use her for something else, like getting access to the library in Canterlot. There are so many directions this fanfiction could take.