They were immediately imprisoned by both the United States and Japan.

Russell Estlack's The Aleut Internments of WWII is a good basic description of what happened. In summer 1942, there were 42 Native inhabitants of Attu and two white residents. When the Japanese arrived, they executed one of the white residents, a man named Foster Jones who sent a radio message (not received) reporting the invasion. The Native residents and surviving white resident, a woman named Etta Jones, were effectively held under house arrest. The native residents of Chichagof Village had their outboard motors confiscated, then returned, and they were limited in their fishing. They were harassed and were the subject of theft by Japanese soldiers. Japanese officers eventually strung a barbed-wire perimeter around the village to protect it from the soldiers.

Etta Jones was taken by the Japanese off Attu within a week of the invasion and imprisoned in Yokohama with 17 Australian nurses and a female plantation owner from New Guinea. The Native residents of Attu were first taken to Kiska, then transported to Japan in September 1942. During the voyage, one of the residents died of a wound suffered during the invasion (she had been shot accidentally).

In their three-year Japanese internment, 21 of the 41 surviving Attu residents died. Only 20 survived to be brought back to the United States. After the war, the American government forbade them from returning to Attu, even though they requested to do so. Instead, they were resettled at Atka, a town in the middle Aleutians.

Kiska was uninhabited except for a 10-man U.S. Navy weather station and a dog named Explosion. All 10 of the sailors were captured by the Japanese (one after 49 days on the lam, living in the wild on the island) and survived the war. Even Explosion survived the war. He was adopted by Japanese soldiers, then left behind when the Japanese evacuated the island. He was re-adopted by American soldiers.

The residents of the Pribilof Islands and the Aleutians west of Dutch Harbor were forcibly evacuated from their homes by the U.S. government in mid-to-late 1942. They were resettled in dilapidated canneries and boarding schools in Southeast Alaska for the duration of the war. While not restricted to these locations (many left for wartime work elsewhere), conditions were completely inappropriate. Many died of disease, some of which was undoubtedly brought on by exposure to cold, wet weather. I attended a memorial service to rededicate a cemetery at one of these locations.

In the 1980s, the U.S. government agreed to compensate the Aleut internees alongside the Japanese-American internees of the war, but most never returned to their original homes, even after the war ended.