In a design innovation reminiscent of the Ion, Saturn added a third door on the driver's side to the 1999 Saturn S-Series coupes. As for changes across all trims, mechanical improvements included adjustments to the powertrain, suspension, and brakes. In addition, prices for coupes experienced a minor decrease. Other cosmetic changes include 2 new colors and new fabric for the SC2. With the new third door on the coupes, the trim lineup increases to 9: the 2 door SC1 and SC2 coupes, the 3 door SC1 and SC2 coupes, the SW1 and SW2 wagons, and the SL, SL1, and SL2 sedans. The SC1, SL, SL1, and SW1 have a 1.9 L, 100 hp I4 engine while the SC2, SL2, and SW2 upgrade to 124 hp. All trims have standard 5 speed manual transmission with the SL as the only one not offering optional 4 speed automatic. Sedans and wagons seat 5 while coupes still seat 4. Gas mileage across trims comes out to around 27 mpg in the city, 37 on the highway. In addition, the trunk holds 11.4 cubic feet in the coupes, 12.1 in the sedans, and 24.9 in the wagons. If you want to avoid paying extra to stay cool, only the SC2, SW2, and SL2 come with standard air conditioning.

Besides the third door on the coupes, Saturn maintained the same core features for the 1999 S-Series while making some minor adjustments. Consumers have the same issues they've always had with the S-Series: excessive oil consumption, cheap materials, and road noise. While some would say that Saturn's frugality re-affirms that you get what you pay for, most Saturn customers would say that the S-Series gives you just enough to do what you need to do.