The Eagle was shown equipped with a special laboratory section, but when the ship lifts off by the rock sample, a regular Eagle was used.
One example of what made this script seem to lack intellect was that the entire landing party was unable to locate Tony (while under the rock's power), when he simply walked from the Eagle straight to the living rock formation and back again.
As Tony (Tony Anholt), in a trance, reenters the Eagle with the rock a wire - possibly providing the power for the rock's illumination - can be seen near his belt.