The missile compartment was configured for support of Naval Special Warfare, and the ship passed its initial SSN Tactical Readiness Evaluation. Following shakedown, the ship was assigned to Submarine Squadron Four at Charleston, SC and won the White "A" for excellence in Anti-Submarine Warfare. Woodrow Wilson was assigned missions in Fleet and NATO Exercises, Atlantic SSN Operations and a primary tasking in the development of new submarine and Naval Special Warfare tactics. In September of 1991, the ship was a key participant in Exercise Phantom Shadow, the largest ever Navy and Special Warfare exercise, which lasted a month in the Western Atlantic and Caribbean. In the spring of 1992, Woodrow Wilson conducted a successful MK 48 warshot SINKEX during her 30th underway since completion of overhaul two years before. CDR Glen Dilgren was relieved by CDR Marshall Page in April of 1992. During her final years of service, the ship continued SSN operations in the Atlantic, Mediterranean, and Caribbean.