Often when I'm working out a scene, I have to come up with two plots: what the characters planned to happen, and what actually happened. In other words, I'm plotting plots as in someone's plan or scheme. It's usually a dastardly plan that my characters must thwart, but occasionally it's the failed plan of my character as well.
In these cases, I have learned to apply the KISS method. Keep It Simple, Stupid. There's no need for the original plot to be this complicated thing, because guess what? It doesn't happen. The plot that actually happens--that's the thing that can be as complicated and nuanced as I want.
Think of The Princess Bride. In that wonderful movie, Vizzini's plot is to start a war. To do so, he is going to kidnap the princess and frame Guilder for it. Simple, huh? Of course, things started getting complicated with the appearance of the Dread Pirate Roberts. And we all know who he was.
Take a more modern example--the movie Stardust. The witch Lamia's plan was to find the star, make her so happy that she shines, and cut out her heart. Instant youth. Only problem is, a lovestruck boy finds the star first, and there's more to that boy than anyone thinks.
In Stardust, we had overlapping plots to add to the complexity. The seven princes--at least the living ones--needed to be the one that finds the jewel that would declare him king. Of course, the star was wearing the jewel, because it knocked her out of the sky. And the star is now with the boy. Individually, each plot is simple. Woven together, it becomes much more complex.
But it's fun!