The flight plan for the Gemini 9 was basically the same as that of its predecessor: a rendezvous and docking with an Agena target vehicle, a firing of the Agena's main engine to take the docked combination into a higher orbit, a number of scientific experiments, and a spacewalk by pilot Eugene Cernan using the Astronaut Maneuvering Unit (AMU).

Once again, the Agena target vehicle exploded after takeoff and a similar, but less versatile backup target vehicle was launched instead. Furthermore, mechanical problems allowed only a rendezvous with the target instead of the planned docking. The EVA uncovered more problems with space suit design, yet lasted a record two hours and eight minutes. The remainder of the flight, which included seven science experiments, was successful. The mission lasted three days, launching Thomas Stafford and Cernan on June 3, 1966.

The attached is a section of Nylon tie line used aboard Gemini 9 to strap items securely into the astronauts' survival packs.