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.
Well, a great plot could be Twilight Sparkle as an Alicorn going on a journey to discover the origin of Alicorn magic. This could involve her meeting ancient Alicorn spirits and learning secrets about her own powers. Or perhaps she gets caught in a time - loop where she has to repeatedly use her Alicorn powers to break free and figure out what's causing it. It could also be interesting if she has to teach other ponies how to use Alicorn - related magic.
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 common theme is friendship. Since Twilight and Trixie are both from the same universe, many fanfictions explore how they can become friends despite their differences. Another theme is magic. Given that they are both magic - users, stories often revolve around their magic skills and how they can learn from each other. Redemption is also a theme, especially for Trixie who has had some not - so - great moments in the original series.
One idea could be that Prince Blueblood has to team up with Twilight Sparkle to solve a mystery in Canterlot. Maybe a series of magical artifacts are disappearing and their combined knowledge and skills are needed to figure out who is behind it.
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.