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 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.
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.
Maybe Twilight Sparkle is forced to use dark magic to save Equestria from an even greater evil. However, she has to struggle with the moral implications. She might have to make sacrifices and deal with the distrust of her friends who are afraid of the dark magic she wields.
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.
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.
Maybe the fanfiction could explore a magical accident that results in a baby - like entity being created between Twilight and Flash Sentry. They then have to figure out how to take care of this new being while also trying to reverse the magic if it's not meant to be. For example, they might seek the help of Princess Celestia to understand what happened.
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.