As Micar points out, you need a villain to drive a plot. I'd suggest that either you start with a villain or two and come up with a plot appropriate to their needs, or you start with a plot and come up with a villain who would want to go through with it - either way is fine.
As far as adding intrigue goes:
Beyond your main story arc and plot, I'd suggest that you can add a new dimension of intrigue to the campaign if you set up a bunch of adventures and things going on unrelated to your main story arc, and then have your villain notice them and try to exploit them. Part of being a good villain is reacting when opportunity knocks, so your villain should exploit that pirate raid as a diversion for the burglary of the palace treasury, and make alliances with the goblins taking over those mines to cut off trade to the south. There probably should be more going on than your main plot in order to add a bit of variety and verisimilitude to your campaign.
In doing this, your group can seemingly "take a break" from the main thread of the story arc, only to find them drawn back into it due to finding the villain's involvement and schemes behind that, too. It can be overdone though; unless he's a compulsive diviner or a god, few villains are omniscient about everything that's going on, and it would be silly if a single villain had his fingers in
every pie. I guess that's where you can add more villains, perhaps even with competing plots, pushing the intrigue further. You might even get into a situation where the PCs find it prudent to temporarily join forces with a "lesser evil" villain in order to oppose a "greater evil" villain, and that's usually an interesting situation intrigue-wise, especially if they PCs have fought their new ally in the past and are cooperating only grudgingly.
