In Spain, his enemies were doing everything in their power to undermine his reputation.

His statements were read more and more coldly, and at last, on the twenty-first and twenty-sixth of May, 1499, letters were written to him instructing him to deliver into the hands of Bobadilla, a new commandant, all the fortresses any ships, houses and other royal property which he held, and to give faith and obedience to any instructions given by Bobadilla.

That is to say, Bobadilla was sent out as a commander who was to take precedence of every one on the spot.
He was an officer of the royal household, probably a favorite at court, and was selected for the difficult task of reconciling all difficulties, and bringing the new colony into loyal allegiance to the crown.

He sailed for San Domingo in the middle of July, 1500, and arrived on the twenty-third of August.
On his arrival, he found that Columbus and his brother Bartholomew were both absent from the city, being in fact engaged in efforts to set what may be called the provinces in order.

The young Diego Columbus was commander in their absence.