The terrorist attacks of September 11, 2001 resulted in death and devastation in three locations, and extraordinary efforts have been exerted to identify the remains of all victims. As mass fatalities go, this one has been unusual at a policy level because the goal has been not merely to identify remains for every decedent, but to identify every bit of remains found so that even small pieces of tissue can be returned to families for burial. While the human impact at the Pentagon and Shanksville, PA was horrific, the World Trade Center site presented a particularly complex challenge for forensic DNA matching and data handling. A complete and definitive list of all those killed is still elusive, and human remains were crushed and co-mingled by the falling towers. Software tools had never been considered for a problem of this scale and scope. New data handling systems had to be created under extreme software development conditions characterized by incomplete requirements specifications, chaotically changing priorities, truly impossible deadlines and rapidly rolling production releases. Partly because of the company's experience with mtDNA tools built for the Armed Forces DNA Identification Lab starting in 1997, the New York City Office of Chief Medical Examiner [OCME] contacted Gene Codes Corporation in late September as existing data-handling tools began to fail. We began work on the project in mid-October, 2001. Our approach to the problem included: Extreme Programming [XP] methodology for functional software development, On-site time and motion analysis at the OCME for user interface design, Evidentiary references between STR, SNP and mtDNA analysis results, and Separate data Quality Control [QC] and software Quality Assurance [QA] initiatives. A substantial software suite was developed called M-FISys, an acronym for Mass-Fatality Identification System.