One plotline could be that the bookstore is a portal to different time periods or dimensions. The Ninth Doctor discovers this accidentally and has to figure out how to control it while also dealing with customers who accidentally stumble into other worlds. Another could be that a villain is after a powerful book in the store that the Doctor has been protecting.
I'm not super familiar with this specific fanfiction, but it could be really interesting. Maybe in this fanfic, the Ninth Doctor's bookstore becomes a meeting place for all sorts of adventures. It could attract other time - traveling characters or people with special abilities. The human aspect of the Doctor might add a different dimension to his character, like he has to deal with more 'human' problems in running the store while still having his Time Lord knowledge.
One interesting plotline could be Harry using his 'ownership' to reform the Hogwarts curriculum. He might introduce new classes like Muggle Studies for wizards to better understand the non - magical world. Another could be him using his influence to improve the living conditions for house - elves at Hogwarts, as he has always been sympathetic to their cause.
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.
One possible plotline could be Izuku having superhuman abilities that are not like the normal quirks in the original story. For example, he might have the ability to manipulate time or space in ways that are completely unheard of in the My Hero Academia universe. This could lead to him being both feared and revered by others.
Perhaps Bella is a shapeshifter in the fanfiction. She can change into different forms, and this ability is both a gift and a curse. She has to hide her true nature from the humans around her, but at the same time, she uses her shapeshifting to solve problems or get out of dangerous situations. This could lead to a lot of secrecy and mystery in the story, as well as some tense moments when she's almost discovered.
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.
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.
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.
Another plotline could involve Megatron using his knowledge from being a Transformer in his new human form. Maybe he uses his strategic skills to solve human problems, like helping in a corporate takeover in a more ethical way than the humans were planning.
One idea could be that the reader is a time - traveler who accidentally crosses paths with the Ninth Doctor. They end up in a historical event that they have to fix together. Another could be the reader living in a world under threat from an alien invasion, and the Ninth Doctor arrives just in time to save them and they then join him on his adventures.