Comiskey started a support group for ex-gays at the Vineyard Santa Monica; with the encouragement of the pastor, Comiskey started his own ex-gay organization called Desert Stream Ministries. In 1981, Comiskey became a pastor in the Vineyard Christian Fellowship. Later, Comiskey and Desert Stream would move and become part of Vineyard Anaheim. In the following years, Comiskey continued his work as a pastor and leader of Desert Stream Ministries. Comiskey cites Leanne Payne as a major influence. Comiskey gives seminars on avoiding homosexual relationships and behaviors and has written four books on the subject; Comiskey's Pursuing Sexual Wholeness became one of the most popular books on the topic. Comiskey and his wife now have four children.
In 2005, Comiskey left Southern California and moved to Kansas City where he continues to lead Desert Stream Ministries.