In 1991 he assumed command of USS Abraham Lincoln (CVN-72) and participated in Operation Desert Storm while deployed during her maiden voyage in the western Pacific and Persian Gulf.

In June 1995, Ellis assumed command of Carrier Group Five/Battle Force Seventh Fleet, breaking his flag aboard USS Independence (CV-62), forward deployed to the Western Pacific and homeported in Yokosuka, Japan.

Ellis' shore and staff assignments include tours as an experimental/operational test pilot, service in the Navy Office of Legislative Affairs, and duty as F/A-18 Program Coordinator, Deputy Chief of Naval Operations (Air Warfare).

[3] Ellis holds Master of Science degrees in Aerospace Engineering from the Georgia Institute of Technology and in Aeronautical Systems from the University of West Florida.

He completed United States Navy nuclear power training in 1987 and is a graduate of the Senior Officer Program in National Security Strategy at Harvard University.