The rendezvous evaluation pod (REP), a 34.5 kg optical and electronic duplicate of the Agena planned for use in later Gemini rendezvous missions was deployed two hours into the flight on the second revolution. About 36 minutes into the evaluation of the rendezvous system, the crew noticed the pressure in the oxygen supply tank of the fuel cell system was dropping. At some point earlier in the flight the oxygen supply heater element had failed, and the pressure dropped from nominal pressure of 850 psia to a low of 65 psia 4 hours and 22 minutes into the flight. This was still above the 22.2 psia minimum but it was decided to cancel the REP exercise and power the spacecraft down. An analysis was carried out on the ground and a powering up procedure was started on the seventh revolution. Over the rest of the mission the pressure slowly rose in the fuel cells and sufficient power was available at all times.

Four rendezvous radar tests were conducted during the mission, starting on revolution 14 on the second day. On the third day a simulated rendezvous with a phantom Agena was conducted. On day five thruster number 7 became inoperative and maneuvering system operation became sluggish. Thruster number 8 failed the next day and the system became increasingly erratic. Limited experimental and operational activities continued throughout the remainder of the mission. Retrofire was made on revolution 120 (one revolution early due to a threatening tropical storm near the landing area) at 7:27:42 a.m. EST on August 29. Splashdown occurred at 7:55:13 in the western Atlantic at 29.73 N, 69.75 W after a total mission time of 190:55:14. Splashdown was 169 km short of the target due to a ground-based computer program error. The crew arrived onboard the aircraft carrier U.S.S. Lake Champlain at 9:26 and the spacecraft was recovered at 11:50.