On March 31, 1941, Amir Abdul Illah, the commissioner of the four-year-old king of the country, who was aligned with the British interest, was overthrown in a coup by Rashid Ali el Gailani, who was friendly to the Axis cause. As Anglo-Iraqi relations continued to deteriorate, the British worried about the fate of the Mosul oil wells they were exploiting. In late March, Iraqis began to encircle the Habbaniya. The British formed two large air formations of 45 and 54 aircraft, respectively, carrying out show of force flights over the heads of the Iraqis. Greek training Officers participated in these flights, including Marcou, but also several students of the School who were in an advanced stage of training. When it became clear on April 6 that the conflict was imminent, the British Headquarters sent an official letter to Wing Commander Vilos asking whether the Greek pilots were determined to participate in military operations on their side. But Vilos was unable to order his men to take part in the war, as Greece was not at war with Iraq unless he received orders from his superiors. On the other hand, however, it was not possible for the Greek pilots to remain inactive since the future of the unit that hosted them was at stake. A meeting was immediately convened between the four instructors, Flt/Lt Georgios Marcou, Flt/Lt Constantinos Platsis, F/O Constantinos Margaritis, and P/O Leonidas Drenas. In the discussion that followed, it was decided by a majority, following a proposal by Drenas and radical disagreement of Marcou, that the Greek instructors will take part in the British operations for a 48-hour period, pending order from their superiors’ Officers in Greece. Regarding the aviation cadets of the Greek group, the decision was made to be used only in auxiliary services. The objections of Marcou regarding participation in the operations were not unfounded. From an International Law point of view, Greece was in a peculiar position to be called upon to engage in a conflict, without having previously officially declared war. In addition, he was called upon to clash with a country whose people, as the Greek aviators had found out, treated Greece with particular sympathy and its unequal struggle against the Axis powers. Also, if the Air Base was occupied, the British would be treated as prisoners of war, under international conventions, while the Greeks would be considered mercenaries and would be executed!

On May 1, the Iraqis issued an ultimatum to the Commander of Habbaniya Air Base demanding immediate surrender, claiming that any plane attempting to take off from the runway would be hit. On May 2, the British, surrounded by 7,000 Iraqis with heavy artillery, decided to surprise them by attacking first. Since dawn, that day, 33 aircraft, most of them Hawker Audax and Hawker Hart single-engine aircraft, along with eight Wellington twin-engine bombers, have been relentlessly bombing their targets in a total of 193 combat sorties. As soon as they recovered from the surprise, the Iraqis retaliated, bombarding the airbase with their artillery, but at the same time, they hesitated to launch an attack against Habbaniya. The result was a hell of a fire at the airport, with Markou and his colleagues risking their lives to get on their planes. Margaritis narrated:

"As we trying to go to our aircraft we looked like grasshoppers, jumping from trench to trench, and then inside the cockpit for take-off."

Flt/Lt Platsis (who flew 30 missions) in at least one case escaped certain death. During the refuel of his aircraft, the airport was hit by Iraqi artillery and his Audax exploded, killing the ground crew who were serving it. Fortunately, he happened not to be close at the time of the explosion. From the first day of the hostilities, the four Greek instructors participated in a series of successful combat sorties. The pilots Platsis, Margaritis, and Drenas, flew with Hawker Audax, while Marcou, flew with a twin-engine Airspeed AS10 Oxford, spotted the positions of the Iraqi cannons, giving their location to his colleagues, who dived-bombed and firing the enemy positions. The Iraqi Air Force tried to react but succumbed to the superiority of British pilots, who prevailed in the air battles. The British soon began hitting targets outside the Habbaniya area in order to hit Iraqi supply routes and communications. In the days that followed, the Greek pilots flew incessantly, participated in dozens of missions, returning many times with their aircraft pierced by enemy fire. Within 14 days, Marcou had carried out 30 combat missions, including bombing and strafing Iraqi troops, fuel tanks, barracks, and vehicles. In at least one case he bombed successfully a column of vehicles that were destroyed. Later, towards the end of the operations, he submitted a personal report and ended his combat flight, for reasons that are not specified. Equally brilliant was the action of the rest of his colleagues, especially Margaritis (45 missions) and Drenas (35 missions), who, among other things, set fire to a fuel depot with 1,000,000 gallons of gasoline and a column of cars carrying ammunition! Drenas in one case was hit and made a forced landing on the enemy lines but eventually returned safely. In the vortex of the war, the Greek aviators, in addition to the stress created by the danger of battle, had to face their anxiety about the fate of their loved ones back home, after the news of the occupation of Greece by the Germans. Eventually, after days of fighting, the Iraqis were forced to end the siege and the British took full control. For their excellent action, the four Greek pilots were awarded the British DFC (Distinguished Flying Cross), accepting the congratulations and thanks of Air Marshal Sir John Henry D'Albiac, who had just returned from Greece, from where he left, on May 28, 1941, shortly before the fall of Crete.