Moffitt is seriously wounded in a raid on a German convoy. The Patrol is far from help and so Troy decides to obtain blood from a nearby German field camp. Dietrich is in charge of the base; Troy encounters him and orders him to help him find a donor. Dietrich sends for Corporal Pennell (guest appearance by teen idol Fabian Forte), a captured Yank deserter. Pennell refuses to cooperate but Troy takes him at gunpoint. On the way back to Moffitt, Dietrich catches up to them and it is up to Pennell to do the "impossible" to prevent them from all being recaptured. He rises to the occasion and they make it back to Moffitt and Tully in time to save Moffitt's life.

Troy raids German HQ and kidnaps Dr. Schneidermann. At the same time Moffitt, Tully and Hitch are captured by Captain Dietrich. Dietrich reveals that Troy is carrying a vial of deadly radium. He urges Moffitt to divulge Troy's destination, bargaining the Patrols' unconditional freedom for the return of Schneidermann. Moffitt, disbelieving the radium story, keeps quiet. However Troy is carrying the fatal vessel. The three Patrollers escape and trail Troy back to the rendezvous, with Dietrich trailing them.

After capturing Dr. Anderson, a skilled Allied physician, Dietrich ends up turning over his staff car in a ravine (during a blinding sand storm). Troy wants to attempt to rescue the doctor but can't because of the storm. He hears Dietrich's distress call but suspects it is a trick. In the end they do make the attempt as they hear that the Germans are going to do the same. They get Dr. Anderson--who is fine--but Dietrich is trapped under the car and badly injured. The doctor tells them that Dietrich is dead but the German groans just before the Patrol leaves. When Troy ends up saving Dietrich's life, the doctor was about to kill him with a murderous dose of morphine, Dietrich tells Troy that Anderson is a double agent. Anderson ends up getting killed just as the Germans arrive to help their captain.

The Patrol ambushes a German courier and finds that his papers contain charts showing desert waterholes and some oases which are unknown to the Allies or the Germans. Suddenly a German patrol attacks, wounding Tully and destroying the Patrol's jeeps, water and weapons. Troy and crew strike out for a waterhole mentioned on the chart. Hours later, near their end, Troy and his men stagger toward an inviting waterhole to find it has been poisoned. On a distant dune they see Dietrich. Tully is near the end, because of his wound. It is up to Troy to negotiate with Dietrich.

When the patrol ambush an Afrika Korps supply column, Troy accidentally wounds a German nurse. Feeling guilty, Troy decides to take her to a German field hospital. The only problem is that on the way she overhears a piece of vital information.

The Rat Patrol uses Moffitt's old flame as a guide to rescue her husband, a French rocket scientist, from the Germans.

Dietrich and his men capture the Rat Patrol and assume their identities, and thus are able to enter an Allied munitions dump.

Troy's brother is captured by a German colonel who was injured in an earlier raid by the Rat Patrol.

Troy and Hitchcock are captured by a German colonel who has a scheme to use them to radio false information back to their headquarters. Meanwhile, Moffitt and Pettigrew's rescue attempts are complicated by an Italian officer who wants to surrender to them.