The research program planned for Mike Foale featured a total of 35 investigations (33 on Mir, two on STS-84, and another preflight/postflight) in six disciplines: advanced technology, Earth observations and remote sensing, fundamental biology, human life sciences, space station risk mitigation and microgravity sciences. Twenty-eight of these were conducted during previous missions and were to be continued, repeated or completed by the end of the STS-84 mission.

Other activities conducted during the mission included investigations using the Biorack facility, located in the SPACEHAB Double Module in Atlantis' payload bay, a photo survey of Mir during docked operations, environmental air samplings and radiation monitoring.