We present an all solid-state Yb:S-FAP laser system running on the three-level laser transition at 985 nm. The pump source was a high fill-factor laser diode bar, with the output reformatted using a two-mirror beamshaping system to produce a rectangular pump beam that focused to a square spot. A nearly on-axis multipassing system was used to obtain four pump passes through a 1.6 mm Yb:S-FAP laser crystal. Gain-switched three-level laser output was achieved with an efficiency of 4.3% with respect to incident pump power. Electro-optic Q-switching produced 0.12 mJ pulses for a pump pulse energy of 11 mJ. Intra-cavity second-harmonic generation yielded a maximum pulse energy at 492.5 nm of 12 μJ.