Launch from Cape Canaveral; landing 500 km east of Cape Canaveral in the Atlantic Ocean.

Former prime crew (Elliot See and Charles Bassett) was killed in an T-38 training airplane crash on February 28, 1966, so their backups Stafford and Cernan became prime crew. Astronauts Lovell and Aldrin became the new backup-crew.

The main goals of this mission were to rendezvous and dock with the Augmented Target Docking Adapter (ATDA) and to conduct extravehicular activities (EVA).

Launch of the ATDA and of Gemini 9A were successful, but the docking with the Augmented Target Docking Adapter ADTA was not achieved because the shroud on the ATDA failed to separate.

EVA by Cernan (2h 07m). The secondary objective of this EVA, evaluation of the astronaut maneuvering unit (AMU), was not achieved. Every work during the EVA took much longer, than expected and he had could not maintain body position. Cernan became exhausted and the face plate fogged over - he had to grope and couldn't see anything. At the end of his EVA he had big problems to return into the capsule and to close the hatch. Stafford had to help him. Cernan later was bitterly disappointed that he had been unable to fly the Air Force's maneuvering unit.

Crew also performed several other experiments, so as bioassay of body fluids (the only medical experiment onboard). A micrometeorite collection package (mounted on the ATDA) should had been picked by Cernan during his EVA. Due of his blindness from the fogging face plate, he only was able to take some photos of this package. Another package was mounted on the Gemini capsule and could be retrieved. Other experiments were the zodiacal light photography and the airglow horizon photography, which were partly successful, but also impaired through Cernan's problems during his spacewalk.

The splashdown, only 3 km far from the recovery ship, the USS Wasp, was broadcast live on TV.