The MOL Mission Module took up most of the spacecraft. It had a length of 11.24 m and was divided into two major bays, the forward section 4.42 m long, and the aft section 6.82 m long. The military experiments it would carry varied from mission to mission and remained largely classified even 25 years later.

On most missions it was believed that the KH-10 optical surveillance system would be carried. This consisted of a telescope with a 1.8 m diameter mirror. This was said to be capable of a 4-inch theoretical ground resolution, 9 inch effective. Film would have been returned in four re-entry capsules during the course of the mission. For extended use beyond the forty day manned mission, solar panels may have been fitted for some missions. It was believed the optical reconnaissance payload for the Mission Module had a lot in common with the KH-9 'Big Bird' unmanned reconnaissance satellite. Work began on this even before the MOL cancellation (perhaps the USAF and CIA could see the writing on the wall). There were also plans for versions of the Mission Module to test side-looking radar, equipped with airlocks for manned EVA operations, satellite inspection, and ELINT. One version, no longer in consideration at the time of the project's cancellation, would have had a long pressurized tunnel going from the hatch in the base of the Laboratory Module to an aft docking collar. This would have allowed two MOL's to dock end-to-end for extended operations.