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I ran out of gas in my 2006 saturn ion. I have replaced the fuel filter and spark plugs. I have cleaned the fuel pump and it is working. But my check engine light is flashing and still does not run like it should.

To prevent this from happening in the future, be sure to never let your gas tank reach anything below a quarter tank. With the Saturn Ion’s, I know you have about a millimeter below the red line before it is Empty. Especially in the winter, if the gas tank is not at least halfway full, water can be submitted inside the tank and freeze over–causing the fuel tank to not work as properly.

I need to know a little more. After you ran out of gas did u change the plugs and fuel filter before you put gas in it and started it? When the check eng light is flashing that means the comp keeps sending the code to the comp because it sees something really wrong. It sounds like a misfire. Did u put the right plugs in the car? Did you gap them to the right specs? It could poss be a clogged injector from sucking crap from the bottom of your tank but that’s rare. If u get it scanned that can at least tell you where to start.