The Kepler Mission Science Operations Center (SOC) performs several critical functions including managing the ~156,000 target stars, associated target tables, science data compression tables and parameters, as well as processing the raw photometric data downlinked from the spacecraft each month. The raw data are first calibrated at the pixel level to correct for bias, smear induced by a shutterless readout, and other detector and electronic effects. A background sky flux is estimated from ~4500 pixels on each of the 84 CCD readout channels, and simple aperture photometry is performed on an optimal aperture for each star. Ancillary engineering data and diagnostic information extracted from the science data are used to remove systematic errors in the flux time series that are correlated with these data prior to searching for signatures of transiting planets with a wavelet-based, adaptive matched filter. Stars with signatures exceeding 7.1 sigma are subjected to a suite of statistical tests including an examination of each stars centroid motion to reject false positives caused by background eclipsing binaries. Physical parameters for each planetary candidate are fitted to the transit signature, and signatures of additional transiting planets are sought in the residual light curve. The pipeline is operational, finding planetary signatures and providing robust eliminations of false positives.