She was working as a doctor in Singapore when the city fell to the Japanese army in February 1942. She tended to the wounded as they were the last of the evacuates by sea on the "SS Kuala" on 13 February 1942. The medical staff were ordered to evacuate despite having to leave wounded behind. They took to lifeboats when the ship came under attack, but as there were only two lifeboats many staff and patients were in the water, where they were strafed by Japanese planes. Thomson had to swim and she was later pulled into a lifeboat. The lifeboats made it to Kabat Island and they then moved on to Senajang Island. She tended to the wounded and rowed the lifeboat despite a leg wound. They were using wood splints and washing wounds in sea water. She arranged evacuation of the wounded to Singkep Island and this in time included herself with a septic leg wound. She went on to Sumatra where she was imprisoned in Japanese camps. The guards stole the Red Cross supplies and she saw her fellow inmates die.