The second prostration means that...
“Said he: ‘Have you come to us to drive us out of our land with your magic, O Moses?’” In this holy verse, another stage of the dispute of Moses (as) and Pharaoh has been reflected. The Holy Qur’an begins this part of the incident with the following statement implying that all the Divine signs were shown to Pharaoh but none of them affected in his dark heart.
The verse says: “And indeed We showed him (Pharaoh) Our signs, all of them, but he rejected and refused.” This meaning refers to the miracles that, at the beginning of his invitation, Moses (as) showed Pharaoh. They were the miracles of the Rod and the White Hand and the inclusive content of his heavenly invitation.
Now we may note to what Pharaoh, the tyrant, the proud, and the obstinate, answered in front of Moses and his miracles, and, as it is the custom of all unreasonable rulers, how he accused that Messenger.
The verse says: “Said he: ‘Have you come to us to drive us out of our land with your magic, O Moses?’” This statement, as Pharaoh declared, is an indication to this meaning that they know that the subject of prophethood and invitation to Monotheism, accompanied with these miracles, are all some plots to overcome their government and that Moses wanted to expel them and the captains from the habitable land of their ancestors.
This accusation is just the same weapon that all the unreasonable rulers and colonialists have had and applied throughout the history. Wherever they found themselves in a danger, in order to defy people alongside their own benefits, they propounded the subject of the danger which threatened the country. Country, in that circumstance, meant the government of those tyrannical rulers, and its existence meant the existence of theirs.