The goal of this project was to develop methods to optimize and control Homogeneous-Charge Compression Ignition (HCCI) engines, with emphasis on diesel-fueled engines. HCCI offers the potential of nearly eliminating IC engine NOx and particulate emissions at reduced cost over Compression Ignition Direct Injection engines (CIDI) by controlling pollutant emissions in-cylinder. The project was initiated in January, 2002, and the present report is the final report for work conducted on the project through December 31, 2004. Periodic progress has also been reported at bi-annual working group meetings held at USCAR, Detroit, MI, and at the Sandia National Laboratories. Copies of these presentation materials are available on CD-ROM, as distributed by the Sandia National Labs. In addition, progress has been documented in DOE Advanced Combustion Engine R&D Annual Progress Reports for FY 2002, 2003 and 2004. These reports are included as the Appendices in this Final report.