The concept of mercy is often proposed as an antidote to the punitive excesses of our current criminal justice system. But this concept is typically presented in generalized, abstract terms that seem unworkable as a pragmatic decision strategy. Its religious origins and associations only add to this impression. In fact, however, if the biblical accounts of mercy are interpreted using the narrative strategy that is featured in current scholarship, an eminently practical decision protocol emerges from these accounts. This protocol diverges from the common or popular view of mercy. It omits the demand for contrition or gratitude on the part of the wrongdoer, viewing this as an effort to exercise domination rather than extending mercy, and minimizes compassion on the part of the decision maker due to its tendency to merge into favoritism. Instead, the protocol recommends that the decision maker deal with the wrongdoer on a direct personal level, suppress any emotional responses such as anger or indignation, and consider the collateral consequences of the proposed punishment. The author describes the way the protocol can be derived from leading biblical narratives about mercy, including the expulsion from the garden, the mark of Cain, Christ and the adulteress, and the prodigal son. He expands on this derivation by analyzing the book of Jonah, rejecting the common view that this work is a satire and treating it instead as a profound inquiry into the nature of mercy. He concludes by applying the protocol he has derived to policy level decisions in the criminal justice system, specifically judicial sentencing, administrative parole and the use of restorative justice.