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Link here It appears that the spacecraft separated from the upper stage while it was still firing, causing that stage to next collide with the spacecraft.
What is certain is that computers on Progress MS-04 interpreted the separation as nominal and initiated a sequence, which would be normally performed upon reaching orbit, including the deployment of the ship’s antennas and the preparation of the attitude control thrusters, DPO, for action. However, moments after the separation, the spacecraft appeared to be struck twice by the rocket stage, which clearly continued its powered flight. The first impact came nearly straight into the aft bulkhead of the ship, then the second hit landed moments later into the side of the vehicle.
The collision apparently caused the spacecraft’s propulsion system, SKD, to shift to the side from its normal position, the temperature inside its enclosure to plummet and the whole vehicle to tumble. The telemetry from the Progress also indicated the activation of its thermal control system, probably in response to a breach in the ship’s transfer compartment.
Why separation occurred prematurely, while the engines were firing, still remains a mystery.