After failing to regain mobility in his arm after two surgical interventions in 1964 and 1967, Carpenter, suffering from avascular necrosis, was ruled ineligible for spaceflight and further deep-sea missions. He spent the last part of his NASA career developing underwater training to help astronauts with future spacewalks. He resigned from NASA in August 1967, and retired from the Navy with the rank of commander in 1969, after which he founded Sea Sciences, Inc., a corporation for developing programs for utilizing ocean resources and improving environmental health.