You take it wrong, as usual. The answer is in the word: All things will be restored on Earth at the beginning of the physical millenial reign. Man's sinful nature will remain, but without the accuser, who will be bound, to focus it, that nature will not be dominant on Earth as it is presently. When Satan is loosed, sin will again rise up to wreak havoc as it now does.
"where did those that are in rebellion at the end of the 1,000 yr reign come from?"
They are on Earth all along. The rebellion is directed by Satan who is loosed at that time.
“All things will be restored on Earth at the beginning of the physical millenial reign.
Psalm 2:6-12, “Yet have I set my king upon my holy hill of Zion. I will declare the decree: the LORD hath said unto me, Thou art my Son; this day have I begotten thee. Ask of me, and I shall give thee the heathen for thine inheritance, and the uttermost parts of the earth for thy possession. Thou shalt break them with a rod of iron; thou shalt dash them in pieces like a potter’s vessel.
Be wise now therefore, O ye kings: be instructed, ye judges of the earth. Serve the LORD with fear, and rejoice with trembling. Kiss the Son, lest he be angry, and ye perish from the way, when his wrath is kindled but a little. Blessed are all they that put their trust in him.”
Isa 11:1-12, “And there shall come forth a rod out of the stem of Jesse, and a Branch shall grow out of his roots: And the spirit of the LORD shall rest upon him, the spirit of wisdom and understanding, the spirit of counsel and might, the spirit of knowledge and of the fear of the LORD; And shall make him of quick understanding in the fear of the LORD: and he shall not judge after the sight of his eyes, neither reprove after the hearing of his ears: But with righteousness shall he judge the poor, and reprove with equity for the meek of the earth: and he shall smite the earth with the rod of his mouth, and with the breath of his lips shall he slay the wicked.
And righteousness shall be the girdle of his loins, and faithfulness the girdle of his reins. The wolf also shall dwell with the lamb, and the leopard shall lie down with the kid; and the calf and the young lion and the fatling together; and a little child shall lead them. And the cow and the bear shall feed; their young ones shall lie down together: and the lion shall eat straw like the ox. And the sucking child shall play on the hole of the asp, and the weaned child shall put his hand on the cockatrice’ den.
They shall not hurt nor destroy in all my holy mountain: for the earth shall be full of the knowledge of the LORD, as the waters cover the sea. And in that day there shall be a root of Jesse, which shall stand for an ensign of the people; to it shall the Gentiles seek: and his rest shall be glorious. And it shall come to pass in that day, [that] the Lord shall set his hand again the second time to recover the remnant of his people, which shall be left, from Assyria, and from Egypt, and from Pathros, and from Cush, and from Elam, and from Shinar, and from Hamath, and from the islands of the sea.And he shall set up an ensign for the nations, and shall assemble the outcasts of Israel, and gather together the dispersed of Judah from the four corners of the earth.”