Yes. 'After' started out as a fan-created story. It caught the attention of many and was transformed into a more formal publication. The fanfic roots can still be seen in its themes and character development.
Not sure. To determine if 'After' is based on a Harry Potter fanfic, we'd need to analyze the plot, characters, and other elements to see if there are clear parallels.
Well, one could create a new story plot after being based on a fanfic. For example, you might develop a new adventure for the characters in the fanfic. You could also create new character relationships. Maybe in the original fanfic two characters were just friends, but after basing on it, you make them into rivals or lovers.
After basing on a fanfic, you can improve the work by adding more sub - plots. The original fanfic might have had a simple main plot. By introducing sub - plots that are related to the main plot, you can add more depth and complexity to the story. For example, if the main plot of the fanfic was about a hero saving a princess, you could add a sub - plot about a power struggle within the villain's camp that is somehow related to the hero's mission.