Bobko's final flight was as commander of STS-51-J, the second Space Shuttle Department of Defense mission, which launched from Kennedy Space Center on October 3, 1985. This mission carried classified payloads for the Department of Defense and was the second time that a Shuttle mission was used solely for Department of Defense activities. This was the maiden voyage of "Atlantis". After 98 hours of orbital operations, "Atlantis" landed on Edwards Air Force Base Lakebed Runway 23 on October 7, 1985. Bobko became the first person to fly on three different Space Shuttles.