Long before the events of the game Miqol was already the leader of the Machina as well as the ruler of the Mechonis, after the attack of the Bionis on the Mechonis, Miqol flew with the other member of his race on the Fallen Arm leaving his son behind.
He is first met once the party has rejoined with Fiora, he is seen inside Junks and he asks the party to kill his son. He then goes on to explain a little more about Egil's history, and that of the Machina themselves.
Later, when the party falls from Mechonis, Miqol rescues them after being warned by Alvis that they were in danger by catching them on Junks. He then flies the party to the Mechonis Core and back again after the events there. He can always be found on Junks, both on the Fallen Arm and, after Mechonis is destroyed, in Colony 6.