The first major event on the mission was the ejection of the rendezvous pod at 2 hours and 13 minutes into the flight. The radar showed that the pod was moving a relative speed of two meters per second.

While out of radio contact with the ground they found that the pressure in the fuel cell had dropped to 138 newtons per square centimeter (200 pounds per square inch). This was lower than it was supposed to operate at and Cooper decided to shut it down. Without power they would be unable to rendezvous with the pod and it could mean a premature end to the mission.

Tests on the ground found that it was possible for the fuel cell to work, even when the oxygen pressure dropped to 49 newtons. However with the fuel cell off, they would only be able to stay in orbit for a day and still have enough battery power for reentry.

It was decided to turn the fuel cells back on and test them by using equipment that required more and more power. These showed that the fuel cells were stable and the crew could continue the mission.

In the meantime, Edwin Aldrin had been working out an alternative rendezvous test. He had a PhD in orbital mechanics and worked out a scheme where the crew could rendezvous with a 'point in space'.

The crew became cold as they drifted. Even with the coolant pipes in the suits turned off and the airflow on low they still shivered. There was also the annoying fact that the stars were slowly drifting by the window, which was disorientating, so the crew put covers on the windows.

As with Gemini 4 they had trouble sleeping with the alternate sleep periods. They still had little rest when they decided to take their sleep periods together.

The phatnom rendezvous came on the third day. It went perfectly even though it was the first precision maneuveres on a spaceflight. They tried four maneuveres - apogee adjust, phase adjust, plane change, and coelliptical maneuver - using the orbit attitude and maneuver system (OAMS).

The ground realised that there was a small problem during the next day. The fuel cell produced water, though this was not suitable for drinking as it was too acidic. It was therefore stored on a tank on board. The problem was that this was the same tank as the drinking water, with the two seperated by a bladder wall. The problem was that the fuel cell was producing 20% more discharge than expected. However it was soon discovered that there would still be room left over at the end of the mission.

On the fifth day a relative major problem occurred. One of thrusters in the OAMS stopped working. This meant the cancellation of all the experiments requiring fuel and none of the solutions worked to getting the thrusters to start working again.

All the medical experiments from Gemini 4 were performed as well as M-1 into the performance of the heart. This involved Conrad wearing inflatable leg cuffs. There was also M-9 which investigated whether their ability to measure the horizontal changed.

S-1 involved Cooper taking the first photographs of the zodiacal light and the gegenschein from orbit. There were also syntopic photography of Earth. One photograph of the Zagros Mountains showed more detail than the official Geologic Map of Iran. S-7, Cloud-Top Spectrometer found that you could tell the height of cloud from orbit.

Retrofire came 190 hours 27 minutes 43 seconds into the mission of Hawaii. They controlled the reentry, creating drag and lift by rotating the capsule. They still landed 130 kilometers short of the planned landing point. But the computer had worked perfectly, the problem was in the programming. Someone had entered the vaule of the Earth's rotation as 360° per day instead of 360.98°.