Your plot is how you say it.

Your story: Skinner is kidnapped by aliens (or a secret government agency? Who knows?) right in front of Mulder's eyes.

Your plot? There are a thousand or more ways to write this story.

If you're feeling humorous, your plot is Mulder sitting around trying to figure out how to rescue Walter and wondering if Walter even wants to be rescued. You see, Mulder's jealous. He's picturing Walter having wild and crazy sex with a bunch of aliens who have Unusual Body Parts, who are phenomenally flexible, and all of who are completely insatiable. He probably assumes they've given Walter the alien equivalent of Viagra, too.

Maybe you had a mytharc episode type story in mind? Skinner's abduction is how you set the stage for a huge confrontation between Mulder and Cancer Man, or the Well Manicured Man or one of the other Consortium Bad Men. Mulder's worried - hell, he's almost insane with worry about Walter. Will he go as far as he was willing to go to rescue Scully? Does he go over the abduction scene in his mind again and again, the way he does with Sam's abduction--looking for clues? What will he offer the Consortium for Walter's safe return?

Your plot might be a fathoms-deep wallow in angst. Walter's been abducted and in your story, Mulder's barely functional at all. His grief is so overwhelming that he can barely make it from one hour to the next without crying. He's convinced that Walter is dead, and now he'll never have the chance to tell the older man how much he loved him. And, typical Mulder, you decide, he thinks the entire abduction is All His Fault. So, he prepares to commit suicide in an unbalanced fit of remorse. (This is, by the way an example of NON-canon Mulder, for those of you who read that particular essay. But it's a Mulder we see a lot in stories.)

Story. What you want to say.

Plot. How you say it.

Any questions?

(For HL fans interested in an example of story versus plot, visit my fiction page, and Ashlyn'spage and read the Variations stories. A friend gave three of us a story idea. We each wrote our own "plot" and the three stories couldn't be more different. Meg's story is accessible from Ashlyn's page, so all three are available for reading and comparison. I even wrote an extra Variation, a slash one, where the original three Variations were non-slash stories. One story. Three plots.
Well, four if you count the smutty one.)