Former Kentucky jockey Rebel Ralston and the rest of the Howling Commandos follow Sgt. Nick Fury on an assignment to rescue a French Underground leader who has been captured by the Nazis and might reveal critical information about D-Day. Once in occupied France, the Howlers meet members of the Resistance and together, they save town hostages from the Nazi firing squad. Led by Marie, they arrive in Louviers where her father Pierre LaBrave is held captive. The Commandos all get caught except for Sgt. Fury who manages to rescue his team just as the Nazis are about to execute them. Together, they capture General von Ritzik and take him back to England.
The Howlers are sent on a mission into Berlin to capture Lord Ha-Ha, an Englishman who was broadcasting propaganda in favor of the Nazis. Unfortunately, the team loses Junior Juniper who is fatally hit during their escape.
The Howling Commandos welcome their new member Percival Pinkerton who is replacing Junior. On their first mission together, they try to capture Dr. Zemo who has invented a Death Ray, but the villain escapes and destroys his own weapon.
Happy Sam sends Sgt. Fury and his commandos on a 72-hour mission to extract Colonel Parker from a Japanese prison in Okinawa. Along the way, they meet the Skipper who takes them across the Pacific aboard his submarine. On the island, the Howlers manage to infiltrate the POW camp and rescue their spy.
Fury and his Commandos are sent across the Channel at Captain America's request to assist them on a mission. Together, they stop the digging of a tunnel by slave laborers which would be used by the Nazis to invade Britain.
Fury and his men are sent by Happy Sam to investigate and destroy a new Nazi missile base that was spotted on the northern coast of Europe. But the decoy base is actually a trap set by Baron Strucker and his new Blitzkrieg Squad whose members are the Nazi counterpart of the Howlers. They try to capture Fury's team but the Commandos manage to escape and reach the beach where their old friend the Skipper picks them up.
After a successful mission in France where they allowed an Allied destroyer to blow up an enemy port, the Howling Commandos are sent to Heinemund on another mission where they stop the Nazis' efforts for the development of atomic weapons.
On the Italian coast, the Howling Commandos meet Major Richards from the OSS who was dispatched to brief them on an escape route so they are able to rescue General Curtis and his men from Massacre Mountain, despite the intervention of a Nazi spy posing as an American war correspondent who was feeding the enemy with Fury's instructions.
Still crushed with remorse for the death of Junior, Sgt. Fury takes the training of his commandos to a new level of intensity. When Fury gets demoted for disobeying Sawyer, the Howlers are sent to Dortstadt to destroy the base under Dum Dum Dugan's command. Everyone is happy when Fury's grade is restored later that week.
The Howling Commandos are sent to North Africa on a mission against Erwin Rommel's army. The mission is aborted by the British army when it is discovered that Rommel is part of a plot to have Hitler assassinated.
Fury and his Howlers are sent by General Durstine to capture Adolf Hitler himself. While the man they take back to England turns out to be a double, Durstine is happy to get proof that Hitler uses doubles.
Happy Sam is sent away for a while and the Howling Commandos must face a new commanding officer, Captain Flint, a hardcore officer who lives by the rule book. During a mission in Normandy, the Howlers show Flint that army books are not a match against field experience.
The Howlers are sent on a mission to locate a buzz-bomb launcher and mark it so the bomber boys can blast it next morning. They are shocked to see Dino deserting in the middle of the mission, but all are relieved when they learn that Fury had ordered him to infiltrate the enemy to ensure the mission's success.
Fury and his men are sent away to investigate on a terrible new weapon developed by the Nazis in a North African secret base. During the mission, Reb is wounded by a bullet while trying to help Dum Dum escape the enemy. As the meet a caravan of Bedouins, the sheik's daughter nurses him. With her help, he manages to convince her father to lend a hand against the Nazis. The Howlers manage to blow up the fortress and all the secret weapons.
While the Howlers are still in the Sahara Desert, Captain Sawyer gives them another mission to track down a missing American patrol who went missing in the African jungle. When they find a native village enclosed in a stockade, they get the natives to fight back the Nazis who had enslaved them and have the enemy surrender.
Nick Fury and his Howling Commandos are sent to Norway where they destroy an enemy supply ship.
After Pamela's death, Nick Fury pushes his team to their limit. Seeing that their sergeant is about to disobey Sawyer's order to take a furlough, they decide to accompany him to Germany where Fury gets his revenge on General von Krummpt, the Nazi officer responsible for his fiancee's demise.
Fury and his men are sent to Scotland where they defeat Baron Strucker and his Blitzkrieg Squad, who have taken over a castle in which British guards have been held as hostages.
Despite their 3-day pass they intend to spend in London, the Howlers join Fury and travel to Czechoslovakia where they rescue the daughter of an Allied scientist, Dr. Zenish, who is held hostage in a camp.
As part of Operation Tidal Wave, Captain Sawyer sends both Nick Fury and Bull McGiveney and their teams on a ground mission to assist Allied bombers in an air strike to destroy oil refineries in Romania. Despite their rivalry, the Howlers and the Maulers manage to collaborate. During their mission, they come face to face with Baron Strucker and his Blitzkrieg Squad and defeat them.
