One idea could be that Trixie and Twilight Sparkle team up to solve a mystery in Equestria. Maybe a powerful magical artifact has gone missing and their combined knowledge of magic is needed to find it.
Another plot could involve Trixie feeling jealous of Twilight's popularity and status in Canterlot. But then they get into a situation where they have to rely on each other, like facing a powerful dark magic force together. Through this experience, Trixie learns to value Twilight's friendship and Twilight learns more about Trixie's insecurities.
A more light - hearted plot could be a competition between Trixie and Twilight Sparkle in a magic show, but things go wrong when a spell misfires and they end up in a wacky alternate dimension. In this dimension, they have to work together to find their way back home while also learning new and strange types of magic along the way.
One idea could be that Twilight Sparkle's daughter discovers she has a unique magic ability that even Twilight doesn't fully understand. This could lead to her going on a journey to find out more about it, meeting new characters along the way.
One plot idea could be that Twilight Sparkle and Fluttershy go on an adventure together to discover a new type of magic in Equestria. Along the way, they face challenges that test their friendship and individual strengths.
One plot idea could be Twilight Sparkle getting cold feet before the wedding and her friends having to reassure her. Another could be a magical mishap during the ceremony that causes chaos but in the end makes the wedding even more special. Maybe an old enemy tries to disrupt the wedding but Twilight's love for her partner overcomes all obstacles.
A plot could involve a race between Thomas and one of Twilight's flying friends. Twilight has to referee and make sure it's a fair race. Along the way, they discover that there are some dark forces trying to disrupt the race, and they have to work together to stop them and ensure the race is completed successfully.
One plot idea could be them going on an adventure together to discover a new type of magic in Equestria. Another could be Timber helping Twilight with a difficult spell she's been trying to master.
A plot could involve Flash Sentry and Twilight Sparkle teaming up to organize a magical event in Equestria. However, things go wrong when a jealous pony tries to sabotage their plans. They must then work together to overcome the obstacles, find the culprit, and still make the event a success. This would show their problem - solving skills and how their different personalities complement each other.
One interesting plot could be that Twilight's dragon transformation is part of a test by a powerful magical being. In her dragon form, she has to complete a series of challenges in a dangerous dragon - inhabited land. The challenges could be related to controlling her new form, using her dragon - specific powers, and also learning about the history of dragons. This would not only test her physically but also her mental and emotional strength.
Some 'Twilight Sparkle fanfic' are set in alternate universes. In one such fanfic, Twilight could be a human in a world where magic still exists but is very different from Equestria. This allows for a whole new set of challenges and character development as she tries to adapt to this new world while still being true to her core self as a learner and a friend.
One idea could be that the twin brother has a different magical specialty. For example, while Twilight Sparkle is great at magic related to friendship and harmony, her brother could be more attuned to magic of the elements in a different way, like having the power to manipulate natural elements more directly. Maybe he could use his magic to help protect Ponyville from a new, different kind of threat that Twilight's magic isn't as effective against.
A plot could revolve around Twilight Sparkle learning some special form of magic from Princess Cadance. For example, Cadance is an expert in love - based magic, and Twilight wants to understand it better to help her friends with their relationship problems. So they have a series of lessons and adventures along the way.