On July 1, 1943, Noor arrived at the headquarters late, only to see almost a hundred SS and Gestapo agents entering the building. She watched helplessly as they led her fellow comrades from the facility and took them into custody. Returning to Paris she reported what she had witnessed but it was too late to fully warn her superiors as additional raids occurred. Most of the top SOE officials and resistance workers had been captured and were now in custody.

Because she had become a key figure in the SOE work, Maurice Buckmaster, the Chief of SOE operations feared for Noor's life and ordered her back to England. Noor refused, staying on in France, determined to continue acting as a much needed radio operator.- For the next three months, Inayat Khan moved from location to location, transmitting messages late in the night to avoid detection.

Her courage and quick thinking helped her to get out of predicaments several times but eventually she was betrayed by a French woman who reported her activity to the Gestapo for 500 pounds.She was caught in the act by Gestapo agents as she tried to send a message to London. She was taken into custody and immediately escaped through a window, trying to move from rooftop to rooftop but was recaptured.

Noor was subjected to extreme interrogation but refused to talk and bravely requested to be shot immediately. When the Gestapo confined her two a room in its headquarters, she collaborated with two other prisoners and escaped from the facility. Just as they were making their getaway from the compound, air raids sirens caused Germans officers to conduct a security check, exposing Noor and her compatriots and prompting their recapture.

Inayat Khan was transferred to Pforzheim Prison in Germany where she was kept manacled to the wall in order to prevent further escape attempts. She was later transferred to Dachau and was ordered to be executed by SS Chief Heinrich Himmler She was executed on September 12, 1944 along with three other women and was posthumously awarded the George Cross by the French government.