The French Air Force of the armistice had also been engaged in other combats, such as in Gibraltar, where raids that had originated in North Africa in September 1940 came to heavily bomb the British installations on "the rock" (taking great care not to hit the Spanish territory), or during the affair of Madagascar where the French had to face British attacks in May 1942. England had feared that this immense "aircraft carrier" anchored off the African Continent would be delivered to the Japanese by Vichy. The last battles of the French Air Force of the armistice took place in North Africa against the Anglo-Americans during operation "Torch" of November 8th 1942.
Then, things began to occur at a fast pace. Admiral Darlan, Pétain's designated successor while passing through Algiers unexpectedly was somewhat influenced by elements of the Algerian resistance, and despite the ambient Anglophobia, he minimized the destruction by ordering a general cease-fire starting on November 10th. On the 11th, Hitler announced to Marshall Pétain that his troops would enter France's free zone. On the 13th and 14th, General Mendigal while inspecting the French fighter groups in North Africa announced to the pilots that they would now fight with the Allieds, with American or English material. Although the Germans and the Italians signed the dissolution of the French Air Force of the armistice on November 27th 1942, it was allowed to survive on the French homeland under the control of the Secrétariat Général à la Défence Aérienne (SGDA), founded in March 1943.
Several decades after this confusing episode about the French Air Force, it is sometimes tempting to establish an over simplified history between those on the Vichy side, (the so called "loyalists") and the outright "collaborators". During those troubled years, it was not all that simple. In Syria for example, the designated enemy was England for certain, but it was hardly conceivable to consider Germany as an allied. Also, the French officers that had been in contact with the Americans since September 1942 were advised on the November 4th that the invasion of North Africa would take place on the 8th! Too short a notice to ensure that the French Air Force of the armistice would not oppose the landing. This situation was somewhat dangerous for the Allieds because, despite being equipped with under performing airplanes, the French pilots had accumulated considerable combat experience.
Those French pilots and crews who a short time ago were divided, fighting on opposite sides, and sometimes ready to kill each other were now on the same side, ready to take on the fight again together against the Axis forces. (Not without conflict however).
The tragically event of Mers el-Kébir certainly played an important and detestable role among the military of the armistice armies towards the British forces and Anglo-Gaullistes. To pass a quick judgement about the French Air Force of those dark years would result in taking a hazardous historical shortcut.
Perhaps François de Labouchère, pilot for the FAFL said it best: "The difficulty was not in doing one's duty, but to discern which was the right duty."