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.
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.
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 that the immortal has some knowledge that the Doctor needs. The Doctor is constantly seeking knowledge, and the immortal, having lived for so long, might hold the key to solving a big problem in the universe. So the Doctor has to convince the immortal to share that knowledge, which might not be easy as the immortal could be very guarded about it.
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.
The Doctor herself is always a very interesting character. Her intelligence, quirkiness and compassion make her a central focus. Her companions are also great. Yaz, for example, is often explored more deeply in fanfiction. Her growth from an ordinary police officer to a time - traveling adventurer is a fascinating arc. Then there's Ryan, with his dyspraxia, which can add an interesting layer to the stories as he overcomes challenges in different situations.
Perhaps they find themselves in a situation where they have to rescue a group of people trapped in a parallel universe. Jack's skills as a former Time Agent and the Doctor's ability to navigate difficult situations would be crucial in this rescue mission. It could also be a chance for them to learn more about each other's pasts and grow as characters.