Charles Fisk began initial discussions with Frances Conover Fitch, Director of Music, in 1983. He wrote: "The side position for an organ is seldom thought of as ideal, yet St. John's is so narrow and so moderate in cubic volume that a well built and well voiced organ should carry easily to the extremities of the building, particularly if an effort is made to get the organ unobtrusively ‘out of the hole’ it now occupies." The contract was signed in 1984, shortly after his death, and the organ, completed in 1989, exists much as he originally envisioned.

The lofty and overhanging Oberwerk is the primary hymn playing division and contains the Principal chorus and the colorful Sesquialtera. The comparatively large Swell is behind the reversed detached console in a heavily constructed box capable of wide dynamic effects. The lush unison stops and colorful reed stops contribute subtle effects, making this an ideal division for accompanying choirs and instruments. The Pedal contains an independent wooden 16' Bourdon, which forms the façade of the lower case and a full-length 16' Posaune standing just behind the Swell.

Charles Nazarian's white oak case, containing details from the original Estey organ, is designed to complement the nearby reredos, designed by Gothic revival architect Ralph Adams Cram.