Another idea is to timeline the plots, this moves the plot along even if the players do not show interest in it. Remember, for every action, there is a reaction.
Also, think about flow charting your clues and steps of your plot. simple yes to advance the players or no to advance the plot. Example, do players find clue 1, if yes; players move on to next step of the plot having a chance to impact it, if no; the next step of plot takes place as scheduled and players hear about it and have to find clues to go to next step.
Note: impacting a plot does not mean stopping it. Result can be a delay based on the level of success the players had to start plan B to continue plot, Ad Hoc to take out the players, or burnt earth to start cover-up.
Also, think about flow charting your clues and steps of your plot. simple yes to advance the players or no to advance the plot. Example, do players find clue 1, if yes; players move on to next step of the plot having a chance to impact it, if no; the next step of plot takes place as scheduled and players hear about it and have to find clues to go to next step.
Note: impacting a plot does not mean stopping it. Result can be a delay based on the level of success the players had to start plan B to continue plot, Ad Hoc to take out the players, or burnt earth to start cover-up.