One interesting plotline could be their exploration of a strange and uncharted planet. They might encounter unique alien species and have to solve puzzles to survive. For example, they find a civilization that has a very different concept of time, and the Doctor and Romana have to adapt to it while also trying to figure out how to get back to their own time and place.
Often, the Daleks can be antagonists. Their goal of universal domination clashes with the Doctor and Romana's efforts to protect the universe. They might be trying to steal a valuable technology or resource that the Doctor and Romana are safeguarding.
One interesting plotline could be Clara accidentally getting trapped in a time loop and the 10th Doctor having to figure out how to break it. He uses his wits and knowledge of time mechanics to save her.
In some versions of this fanfiction, the Master of Death might be after a powerful artifact that the 9th Doctor is also interested in. The Doctor wants to use it for good, to save lives and protect the universe, while the Master of Death wants to use it for destruction. This leads to a race between them, with the Doctor trying to outsmart the Master of Death at every turn.
One possible plotline is that they meet in a time - locked situation. They have to work together to break the time lock. Another could be that they meet because of a shared enemy that has somehow found a way to target both of their timelines. They would then have to put aside their differences and use their individual strengths to defeat the enemy.
One possible plotline could be the 11th Doctor and Rose exploring a new and mysterious planet together. They might encounter strange alien species and have to use their wits to survive. Another could be them reuniting after a long time apart and having to deal with the changes in their relationship. Maybe Rose has new skills or experiences that the Doctor has to get used to.
Another plotline could be the aftermath of the kiss. Maybe the Doctor is conflicted because he knows his nature as a Time Lord and the complications it could bring to their relationship. Clara, on the other hand, is determined to make it work. This creates a lot of emotional turmoil and interesting character development as they navigate their new relationship status.
Perhaps Naruto discovers a new medical jutsu that combines his chakra control with traditional medical knowledge. This could revolutionize the medical field in the Naruto universe. He might use it to heal previously incurable diseases or injuries, and in the process, gain the respect of the medical community. This could also lead to some interesting interactions with other medical ninja, like Shizune or Tsunade.
In some fanfictions, the 10th and 11th Doctor are brought together by a time anomaly. They are forced to cooperate to fix it, and along the way, they encounter old friends and enemies. The contrast between the 10th's more traditional style and the 11th's more zany approach creates interesting dynamics. They might also have to deal with the consequences of their previous actions in different timelines, which adds an extra layer of complexity to the story.
One interesting plotline could be Rose and the Doctor exploring a lost civilization. They might encounter strange creatures and have to solve puzzles to escape. Another could be a time - travel adventure where they go back to a crucial moment in history and accidentally change something, then have to fix it.
One interesting idea could be exploring the Doctor's internal conflict during the regeneration process. He might be grappling with memories of his past selves and the adventures he had. Another could be how his companions react to the sudden change. They may be in shock or try to help him through the difficult transition.