You left out the part where the CEL flashed on and off.

The "rough running" is because the ECU has turned off cylinders to prevent damage to the cats. They reset when the car is shut off and restarted.

Your post is cryptic enough to include most every possibility.

How many miles on it? What maintenance have you done (and deferred)? How long has the problem been going on? Has it gotten worse? What other symptoms have been cropping up along the way? Have you always run premium unleaded?

No matter what else, the first place to start is to check the codes. That will at least give you a starting place.

Good luck.