Al Qaeda did not have a presence in Iraq until after we invaded and occupied Iraq. There's a good documentary available called "The Road to 9/11" which details the defining moment when OBL turned against us (he was once an ally). When Iraq invaded Kuwait, OBL volunteered to the Saudi Arabian gov't his services and offered to kill Hussein. There was no love between Hussein and OBL. He took it as an affront on his honor as well as an insult to Islam when Saudi Arabia rebuffed his invitation and allowed US troops into Saudi Arabia for the 1st Gulf War. He viewed Saudi Arabia as "Holy Land" and was infuriated that the Saudis would allow a western power to occupy it.