It is shown that the long-term holding under the peak load during the indentation of Si (100) leads to the creep of material even at room temperature. This becomes possible due to the phase transition into a more plastic metallic β-Sn phase. The end structural phases in the indentation zone were studied by the micro-Raman spectroscopy. It was discovered that they are affected by the longer holding under the load. Thus, more intense peaks were detected for the amorphous (a-Si) phase in the depth of indentation, as compared with those observed for short-holding indentations. It is suggested that this effect is caused by the activation of the dislocation mechanism in the a-Si formation as a result of the longer action of sear stresses under long-term holding. This fact induces some changes in the kinetics of the events of unloading, which reveal a trend to the formation of “kink pop-out” events instead of the typical “pop-out” and “elbow” events.