To understand the Muslim Brotherhood and Al-Qaeda you need to see them as ideologies and not as organizations. If you see them as organizations you will perceive them as something a lot more concrete than they really are.
You need to see them like the Capital of Karl Marx, which is simply a book, an ideology, which can be used by anybody.
The Muslim Brotherhood is what we call “political Islam”. It represents a socialist economic model, with the Koran as the country’s constitution. But the Muslim Brotherhood supposedly wants free speech and political elections in the country. We do not actually have an example of Political Islam that allowed a free society to develop, but theoretically speaking that’s what the Muslim Brotherhood asks for.
Moreover the Muslim Brotherhood leaves some space for cooperation with the Crusaders (NATO) and Muslim apostates i.e. Muslim leaders who cooperated with the Crusaders.
Al- Qaeda on the other hand does not leave any space for free elections, neither for cooperation with apostates i.e USA, France or Muslim apostates ie. the Saudi King or the Egyptian President.
Al-Qaeda, like the Muslim Brotherhod, also wants the life of the Muslim people to be governed by the Koran.
Many times in the past both the Muslim Brotherhood and Al-Qaeda have been used by Muslim countries against other Muslim countries, or against NATO, or against internal opponents.
The Muslim Brotherhood and Al-Qaeda are communicating vessels, and the best example is Ayman al-Zawahiri, the leader of Al-Qaeda. Zawahiri, an Egyptian, was a member of the Egyptian Muslim Brotherhood from a very early age, but at some point he went to Al-Qaeda, and he even became the leader of Al-Qaeda after the Americans killed Osama bin Laden in Pakistan in 2011.
The leader of Al-Qaeda is charged with the duty to coordinate the various branches of Al-Qaeda on common interests, whenever that is possible. You should not think the leader of Al-Qaeda like someone who has total control over the whole franchise network.
The important difference between Al-Qaeda and the Muslim Brotherhood is that the Muslim Brotherhood is used to overturn an opponent with elections, while Al-Qaeda is used to attack an opponent with terrorism, when you cannot overturn him with elections.
I would like to give an example.
The Syrian dictator Bashar al Assad belongs to the Alawite minority of Syria, and he also governs the Sunni majority of Syria. The Turks and the Arabs wanted to use this Sunni majority to take control of the country, in order to block Iran and to construct the Sunni energy corridor i.e Qatar-Turkey.
Therefore with the Arab Spring of 2011 the Turks and the Arabs were calling for democracy and free elections, and Assad, who was backed by Iran and Russia, was not willing to go to free elections, because the Alawites are a minority and he would lose them. Therefore the civil war broke out.
But if the Alawites were the majority of Syria, and the Turks and the Arabs could not overturn Assad with elections, and the Iranians and the Syrians were to construct the Iran-Syria pipeline, which would hurt the Turkish and Arab interests, the Turks and the Arabs would use Al-Qaeda, and Al-Qaeda would accuse Assad of cooperating with the Crusaders, and therefore they would attack Assad’s pipelines. Therefore with the conditions that prevailed in Syria the Turks and the Arabs preferred to use the Muslim Brotherhood to gain control, and when that did not work they invaded Syria and started using Al-Qaeda and ISIS.
Map Sunni VS Shia Pipelines
Gamal Nasser and the Muslim Brotherhood
In the 50s and 60s the Egyptian socialist dictator Gamal Nasser, together with the Syrian socialists, were trying to conquer Israel and Lebanon, in order to block the Iranian oil from reaching the Mediterranean Sea through Israel (Eilat-Ashkelon Pipeline), but also to block the oil of Saudi Arabia from reaching the Mediterranean Sea through Lebanon i.e. the trans-Arabian pipeline (Saudi Arabia-Jordan-Lebanon).
That way Egypt and Syria could charge a lot more for allowing the Iranians and the Arabs of the Gulf from exporting their oil to Europe through the Sikl Road. To retaliate, the Arabs of the Persian Gulf were using the Muslim Brotherhood in Egypt and Syria in order to overturn Gammal Nasser and his socialist allies in Syria.
Map The Legacy of Gammal Nasser
Iran, Sudan, Saudi Arabia
The Iranians and the Sudanese supported Al-Qaeda attacks against the Saudi King, but they also support the Muslim Brotherhood against him, asking for free elections, with the help of Turkey, and Qatar. Actually that was until 2015, because in 2015 both Turkey and Sudan received billions of dollars from Saudi Arabia and they relaxed their stance.
Map Sudan-Saudi Arabia Pipelines
In Egypt, Turkey, Iran and Qatar supported the Muslim Brotherhood during the Arab Srping, and they presented it as something new, putting on the table the issue of free elections, which was something exotic for the Egyptians, since the Egyptian socialists were not allowing elections. Therefore the Turks, the Iranians and the Qataris tried to overturn a rival, and a Saudi ally, with elections and the Muslim Brotherhood. They were also greatly supported by the leftist channel Al-Jazeera, which belongs to the Emir of Qatar.
In Afghanitan the Iranians and the Arabs are using Al-Qaeda to perform terrorist attacks against the Americans, because they wanted to bring the oil and gas of Central Asia to India.
Al-Qaeda in Africa (AQIM)
Al-Qaeda in Africa is something very different from Al-Qaeda of Pakistan, and it is anti-French instead of anti-American, and it is mainly supported by Iran, Sudan, Turkey and Hezbollah, which are four enemies of France. Al-Qaeda in Africa is performing terrorist attacks against many French targets.
When we talk about the Muslim Brotherhood we talk about overturning an opponent with elections.
When we talk about Al-Qaeda we talk about attacking an opponent with terrorism.
Who supports Al-Qaeda and who supports Muslim Brotherhood depends on the individual countries.
A poor Muslim can be bought from Al-Qaeda, as a terrorist, or from the Muslim Brotherhood as a voter, with money that comes from any Muslim country.
Al-Qaeda = Terrorist Attack to an Opponent
Muslim Brotherhood = Attacking an Opponent with Elections