Here to steal your thunder some more:
While Neo wrote this guide for roleplays, much of the information is directly applicable to fanfics, especially regarding setting, and a lot can be applied to plot as well.
Imho, the best way to make a plot is to first create your setting, then create your conflicts, characters, and factions (if they exist), and then come up with a vague idea of where you want the story to go. After you have all that set up, just imagine how each of the characters act and interact in their situations in order to resolve the conflicts. In this way, plot grows from the elements of setting in characterization, resulting in a natural series of events that follow logically from your characters, rather than an artificial storyline where characters are forced to constrain to a certain pre-determined plot. Characters drive the plot, after all, and a lot of published fiction writers start off with an idea of where they want to go but end up somewhere completely different because of how the characters behave.
If you get stuck, introduce a new conflict or character to shake things up a bit and get things moving. And watch out for plot holes.