Perhaps they could time - travel to a point in time where their friendship was just starting to form. They could see how their early interactions unknowingly set the course for all their future adventures. Or, they could be sent to a time when a great villain from their present was a young and innocent person, and they have to decide whether to try and change the villain's future or let things play out as they originally did.
One idea could be that Kim and Ron get stuck in a time loop within a particular historical event. They have to keep reliving the same day until they figure out how to correct an anachronism that's disrupting the time - space continuum. Another could be that they travel to the future and see versions of themselves that have changed in unexpected ways due to different life choices.
Maybe in the fanfiction, Kim and Ron find a hidden power within the time - traveling device during 'Sitch in Time'. This power allows them to visit different key moments in their past adventures but also attracts the attention of a new villain who wants to steal this power for their own evil plans. So they have to protect this power while still trying to fix any disruptions in time.
Monkey Fist is often a popular choice. His villainous nature and his connection to martial arts and ancient artifacts can add a lot of intrigue to a time - travel based fanfiction. He could be chasing Kim and Ron through different time periods, trying to steal some powerful relic.
Perhaps in this fanfiction, Kim might lose some of her powers during the time - traveling adventures in 'a sitch in time 2'. She then has to rely on her wits and the help of her friends like Ron and Rufus in a more creative way. For example, she might use her knowledge of history to outsmart the bad guys instead of just relying on her usual martial arts and gadgets.
Their relationship could develop more quickly in the fanfiction. For instance, during the 'Sitch in Time' events, they might have a moment of realization where they understand their feelings for each other more deeply due to the high - stakes time - traveling situation. They could start to act more like a couple earlier than in the original story.
One plot idea could be their adventures as a married couple fighting villains together. Maybe they have to deal with a new super - powered enemy while also juggling their married life, like who does the dishes when they come back from a mission. Another idea is that they go on a honeymoon that turns into a mission to save the world.
One idea could be a story where Ron accidentally discovers a new power and Shego, instead of being an enemy, decides to help him control it because she's intrigued. Meanwhile, Kim is a bit suspicious of their newfound alliance.
Perhaps in the fanfiction, they decide to have a destination wedding. But on the way to the location, they get caught up in a mystery that they can't resist solving. So, instead of focusing on the wedding, they are off on an adventure. This adventure could strengthen their bond even more and make their wedding, when it finally happens, even more special.
There could be a time - guardian character. This character could be an ancient being that has been protecting the timelines and appears to help Kim understand the true nature of time - traveling and the rules she must follow to set things right.
One idea could be that Ron goes back in time and accidentally changes a major event at Hogwarts, like preventing the formation of the Marauders. So then all the events related to them in the original timeline, like the creation of the Marauder's Map, are affected. This would lead to a whole new set of adventures for Ron as he tries to fix what he has broken.
Another interesting concept would be for Kim to travel to the future and see what has become of her friends and family. She might discover that her actions in the present had unforeseen consequences in the future, and she has to find a way to fix things. For example, Ron could have become a super - villain, and Kim has to figure out why and how to turn him back.