Derb, the enemy is united. You have to ignore a ton of evidence (much of which I laid out in this piece) to suggest otherwise. Al Qaeda has had an understanding with Iran regarding mutual non-aggression, training and materiel, for over a decade. It has gotten explosives training and other assistance from Iran and Hezbollah since the early 1990s. The 9/11 Commission says our most recent intelligence indicates al Qaeda may have been complicit in Iran/Hezbollah’s 1996 bombing of Khobar Towers in Saudi Arabia (killing 19 American airmen). Iran/Hezbollah facilitated the travel of the 9/11 hijackers in the run-up to the attacks. Iran allowed senior members of al Qaeda to escape into Iran during the U.S. invasion of Afghanistan and has given them safe-harbor ever since. And Iran has helped both al Qaeda and Shiite elements in Iraq kill American soldiers.
There is more evidence of Iran/Qaeda cooperation than there was of, say, German/Japanese collaboration before we fought them jointly in WW-II. There is, moreover, less that divides Sunni terrorists and Shiite terrorists than there was dividing the U.S. and the Soviet Union when we fought jointly against common enemies in WW-II. When it comes to the United States, there is far more in the way of ideology and methodology that unites Iran and al Qaeda than there is that divides them. That is why they have been working together for nearly 20 years.