Biggles stumbles across an enemy plan to destroy British shipping in the Indian Ocean. Noticing a coincidence in bad spelling, his linking of three separate ship disappearances leads Colonel Raymond to charge him to investigate. Biggles is given the temporary rank of Air Commodore (hence the title) and command of a destroyer.

The planned use of a decoy to lure the bandits fails when the bandits sink it. However they persevere, and eventually discover a secret submarine base on an island in the Mergui Archipelago. Notwithstanding a few distractions, the team manage to destroy the sub, and its base by using their own mines. They all manage to escape just before a secret stash of poison gas makes the entire island uninhabitable.