Largely upon their recommendation, the President appointed a second commission, headed by Judge William Howard Taft to carry on the work of organizing civil government which had already begun under military direction and gradually to take over the legislative power.

The Military Governor was to continue to exercise executive power.

In 1901, Congress at length took action, vesting all military, civil, and judicial powers in such persons as the President might appoint to govern the islands.
McKinley immediately appointed Judge Taft to the new governorship thus authorized.

In 1901 in the "Insular Cases" the Supreme Court also gave its sanction to what had been done.

In legislation for the territories, it held that Congress was not bound by all the restrictions of the Constitution, as, for instance, that requiring jury trial; that Porto Rico and the Philippines were neither foreign countries nor completely parts of the United States, though Congress was at liberty to incorporate them into the Union.
There was, however, no disposition to incorporate the Philippines into the United States, but there has always been a widespread sentiment that the islands should ultimately be given their independence, and this sentiment has largely governed the American attitude toward them.
A native Legislature was established in 1907 under Governor Taft, * and under the Wilson Administration the process toward independence has been accelerated, and dates begin to be considered.