Launch from Cape Canaveral; landing 1330 km southeast from Cape Canaveral in the Atlantic Ocean.

The main goal of this flight was again to dock with an Agena target vehicle. Secondary objectives included docking practice, an EVA, 11 scientific experiments, docked maneuvers, a tethered vehicle test, demonstrating automatic reentry, and parking the GATV.

The launch was postponed twice: On September 09, 1966 due to a small leak in the first stage oxidizer tank of the GLV, and on September 10, 1966 due to a suspected malfunction of the autopilot on the Agena capsule.

The docking with the unmanned Agena target vehicle GATV-11 was completed after five flight maneuvers and only 94 minutes after the launch. There were no fuel problems and the crew began docking practice (two dockings and re-dockings of both astronauts).

Two EVAs were performed by Richard Gordon on September 13, 1966 (0h 38m) and on September 14, 1966 (2h 08m). In the first EVA he attached the tether from the GATV to the spacecraft docking bar, but became fatigued too, even the GATV was modificated with handrails. The face plate of his helmet fogged and this EVA was shortened. The whole complex of two spacecrafts was then brought up to a high apogee record of 1.360 km, using the boosters of the Agena target vehicle. After two orbits the Agena was fired again for 22.5 seconds to lower the Gemini-Agena back down to a 287 x 304 km orbit. The spacecrafts were then redocked and the joined pair was brought into a rotation to build a small gravity in the spacecrafts. The rotation rate checked out at 55 degrees per minute, and the crew could test for a minute amount of artificial gravity, but they did not sense any physiological effect of gravity.

All in all 12 experiments were performed (9 scientific and 3 technological), but only two photograph experiments were new. The other seven - weather, terrain, and airglow horizon photography, radiation and zero-g effects, ion-wake measurement, nuclear emulsion, and the ultraviolet astronomical camera - and all three technological experiments - mass determination, night image intensification, and power tool evaluation - had already been assigned to previous missions. The night image intensification was enjoyed by the astronauts, but were also a little bit handicapped due to a dirty window on Charles Conrads site.

At the end of the mission the first fully automatic controlled reentry was performed. The recovery ship was the USS Guam.