FilmProf - I had the same issues with the 3 lights on once before but it was my fuel cap, it just had to be tightened.
But then last month, I had the 3 lights again and it was chugging. It ran and got us around but it was terrible. I did a ton of research about this and it seems like the coil pack on the spark plugs (scion’s have this instead of a distributor cap) were bad. I took it to AutoZone for a free diagnosis. It said I had a misfire in #2. The first thing I did was replace my spark plugs. (well my husband did) The car was still “chugging”. So after days of pouring over chatrooms about scions, I found someone with the same problem and bought a coil pack on ebay. Normally they cost $200 or so. I found them for $68 with shipping! Replaced them and all of my lights turned off after about 5 miles of driving with the new coil pack. Super easy to replace…just “plug and drive” really.
Good Luck!