Progress M-39 linked up with the aft docking port of Mir on September 01, 1998 at 05:34:58 UTC. Approach and docking were executed in the automatic mode with the system Kurs. Gennadi Padalka reported distances and approach speeds and that he had seen how the engines of Progress M-39 worked. Sergei Avdeyev observed the approach through a porthole. TsUP ordered the cosmonauts to be alert to evacuate if this in case of an emergency was necessary. If he would give this order they had to leave immediately without doing anything. He assured the crew that the approach process was proceeding normally. The cosmonauts had checked the airseal. All was normal. TsUP asked how the quality of the atmosphere inside the Progress M-39 was. Gennadi Padalka said that they had no remarks about that.

After the return of the freighter Progress M-39, the cosmonauts were able to execute a number of experiments. From September 01, 1998 until September 03, 1998 they worked on geophysical, astrophysical and medical experiments. During the geophysical experiments they used the lidar Alisa. Apart from medical experiments the cosmonauts also underwent routine check-ups of their cardiovascular system.

Gennadi Padalka and Sergei Avdeyev performed an EVA, in fact an IVA, on September 15, 1998 (30m) into the module Spektr. They reconnected some cables for the solar panel steering mechanism. The task during the EVA was relatively easy. The cosmonauts had to connect a few cables to an interface for the steering of solar battery number 3 of Spektr. However, the work was not limited to these 30 minutes for an EVA requires a lot of preparations. For instance, the crew had to prepare the transport ship Soyuz TM-28 for an eventual emergency departure. And after the EVA the Soyuz TM-28 had to be conserved again.

The cosmonauts executed astrophysical and geophysical experiments. They used the Mariya spectrometer in the Module Kvant1 to study the generation of high energetic particles in space and the in radiation belts around the earth. Medical check-ups and experiments revealed that the health and physical condition of the crew is excellent. During a private conversation Sergei Avdeyev said that he expects to return to earth towards the summer of 1999.
TsUP and the crew regularly discussed problems regarding the oxygen production for Mir's mini atmosphere. Every day the cosmonauts were engaged in the functioning of the Elektron oxygen generators. These systems did not fail, but it was clear that the crew did not trust the automatic functioning of them, and took over manually at every given moment.
On October 10, 1998 TsUP spoke about the possibility that the CO2 amount in Mir's atmosphere was too high. Telemetry gave a value of 5.9. Gennadi Padalka said that nothing was wrong and that they still felt excellent. Sergei Avdeyev checked the Vozdukh CO2 filter and did not find anomalies. Later the value had been increased to 6.0 and the crew took counter measures by using ventilators to blow the air through the whole complex. This did not help. To decrease the CO2 amount the crew got orders to adjust the Vozdukh scrubber in the Base Block.