The US had a whole plan to invade Taiwan instead of the Philippines, called Operation Causeway. The plan was the brain child of Admiral Nimitz, and was submitted March 1944, which planned to take Penghu first, then land at Kaohsiung and sweep upwards towards Taipei. Kaohsiung was the first target because it was a major Japanese naval base.
Admiral Nimitz saw Taiwan as a great threat to the US navy, especially since Taiwan’s position makes it the perfect Japanese airbase to attack US ships and bomb China. Taiwan also served as the major food supply for Japan. Admiral Nimitz had a priority to neutralize it. The plan had President Roosevelt’s support, and the Tenth United States Army was formed to accomplish the task.
In case Northern Taiwan proved too difficult for the Tenth Army alone, the US planned to bomb Taipei into submission with mustard gas or the atom bomb.
The Japanese also learned of this, and began distributing gas masks all over the island.
General MacArthur had a different plan though. He wanted to make good of his “I’ll be back” promise, and fought Nimitz over whether to invade Taiwan or the Philippines.
By June of 1944, the US retook the Mariana islands, which allowed B-29s to bomb the Japanese mainland. So there was less of a need to use Taiwan as an airbase to bomb Japan.
MacArthur argued that the Philippines would be much easier to retake, as the US had ruled the islands for a long time, and there are plenty of friendly guerilla fighters that would be on the US’s side.
In the end, Roosevelt was persuaded by MacArthur to cancel Operation Causeway. Instead, a series of bombings of Taiwan commenced to pave the way for the invasion of the Philippines. All major naval bases were hit, including Hsinchu which produced naval fuels.
To further eliminate aerial threats from Taiwan airbases, the US navy launched a full air assault on the island with 17 carriers. Formosa Air Battle began on October 12 1944. During the battle, the US navy realized it had full air superiority. Most skilled Japanese pilots were killed in previous engagements, and although the Japanese were able to put together over 1,000 planes, very few pilots were skilled enough to do anything with them.
The Japanese navy also realized it no longer can stand up to US fighters. Both the Formosa Air Battle and the failed Operation Sho to destroy the American navy was a turning point for Japanese tactics. Kamakazi was devised after the Formosa Air Battle. The first Kamakazis were flown from Taiwan (usually Hualien) to stop the invasion of the Philippines.
The Formosa Air Battle dismantled Taiwan’s air defenses, and opened up Taiwan for future bombing raid. The largest one being March 1945’s Raid on Taipei, which killed more than 3,000 civilians. The raid also damaged the Governor-General’s Building (today’s Presidential Palace) and Longshan temple. Duds from the raids were excavated even well into 2009.
There are many ruins of Japanese fortifications around Kaohsiung to prepare for Operation Causeway.
Someone mentioned the Takasago Volunteers, which were a special unit made up of Taiwanese Aboriginals, were especially effective for island battles. At least 500 of them joined the Japanese efforts to invade the Philippines as early as 1942. By the end of the war, more than 4,000 Taiwanese aboriginals had fought in WW2. More than 3,000 of them died in the jungles of New Guinea. Although called Volunteers, towards the end of the war, Japanese were forcing teenage Aboriginals to fight in the Philippines.
The last Japanese holdout to be found after WW2 has ended was a Pangcah from E’tolan (Dulan Taidong). I’ve written a thread on him here: