[7] After shakedown training, Flier departed New London, Connecticut, in early December 1943 bound for the Panama Canal.

While she was on the surface in the Caribbean Sea nearing the approaches to the canal, an Alied merchant ship mistook her for a German U-boat and opened gunfire on her, firing 13 rounds, but she escaped into a rain squall without suffering damage or casualties.

USS Macaw (ASR-11), a Chanticleer-class submarine rescue ship, attempted to pull Flier free but ran aground herself and sank.

[11] The discovery of a Gato-class submarine was made during an expedition by YAP Films, based in part on information provided by a survivor of the sinking of Flier.

Further research by the Naval History and Heritage Command revealed that no other submarine, American or Japanese, had been reported lost in that general vicinity.

In addition, footage of the wreck showed a gun mount and radar antenna, both of which were similar to the same equipment seen in contemporary photographs of Flier.