In 1956 Ellis was made captain of the Navy's new supercarrier USS Forrestal. He commanded the ship during its inaugural cruise and subsequently was fleeted up to Rear admiral on July 18, 1958. His first post as a two-star admiral was Chief of Staff to Commander Carrier Division 6. Ellis stepped back into a command role with his appointment as Commander Carrier Division 2 in 1961. On June 2, 1964 he was given a third star and Vice admiral rank, and put in charge of the Sixth Fleet. After two years serving in this capacity he was relieved of his command and awarded the Distinguished Service Medal. Specifically recognized in his full citation are Ellis's adroit management of an Atlantic command at a time when the Vietnam War pulled increasing Navy resource to the Pacific; and the swiftness with which he assisted in the recovery of a hydrogen bomb lost off the coast of Spain. Ellis's final position within the Navy was as Chief of Staff to the Supreme Allied Commander Atlantic, a post he served in during his last year of service, 1968. He died in a Norfolk, Virginia hospital on September 26, 1982 as a result of cancer.