Answer: You probably need a little bit of a historical perspective to maybe understand it properly. For thousands of years countries have fought wars. Sometimes for land, wealth, differences in political beliefs and a lot of them have been over religion.
I would argue that the reason for the attack, as with similar attacks is part political and part religious. 6 to 700 years after the death of Christ for example the Muslim Conquests saw Islam playing a dominant force throughout the middle east, Asia and into Europe.
This played a large roll in the downfall of the Roman Empire which from about 300 years following the death of Christ had been important in the spread of Christianity.
Now jump forward a few hundred years and you have the Crusades which saw Christian warriors seeking to take back holy lands from the Muslims. Now although this was almost a thousand years ago, for the hundreds of years since then wars have been fought over lands and beliefs relating to this, Israel and Palestine being a perfect example. Now the 9/11 terrorists are Muslim, and their beliefs are different from those of the US which is largely Christian. But more than that the are radical Muslims who take their beliefs to extreme points.
Because of this they disagree with the society that the US has, based on what they see as money, greed, sex etc. So just like the holy wars all those hundreds of years ago they seek to punish the USA for its beliefs by waging Jihad or holy war. In its extreme they will not stop fighting jihad until they take over all non Muslim countries and spread Islam and Islamic law all over the world, and they are willing to fight and die until this happens. This would be the religious aspect.
For the political aspect you have to jump back 10-years before you were born. Back then Russia (or the Soviet Union) was still a dominant power and sought to spread socialism throughout the world just as the US seeks to spread democracy throughout the world. As part of this process in 1979 the Soviet Union invaded Afghanistan.
With the Cold War between Russia and the USA in full swing the US had been seeking to undermine Soviet influence in Afghanistan by funding anti-Soviet factions as leadership at that time was pro-Soviet. It worked and in 1979 the pro-Soviet government was overthrown but naturally the Russians didn't like this and invaded. As part of the Reagan Doctrine, which basically said that anti-communist forces would be supported anywhere in the world, the US actually helped fund, arm and equip the Mujahideen (freedom fighters who formed the basis for the Taliban which included people like Osama Bin Laden, who were essentially CIA trained) to fight against the Russians. The problem is by 1989 when the Russians had been defeated and left Afghanistan the Taliban was a powerful force and developed a stronger religious ideology.
But in 90s the US backed off from Afghanistan and then voiced opposition to the Taliban along with other international groups and governments. It also started to help track down and arrest Islamic terrorists and it was from this time that things began to escalate.
There were actually several Al Qaeda attacks before 9/11, a 1992 hotel bombing in Yemen, the 1993 World Trade Centre bombing in New York, in 1998 when terrorists associated with Osama Bin Laden bombed 2 US embassies in Tanzania and Kenya. And as a result of this one however the US responded and launched a series of cruise missile attacks on several terrorist training camps in Afghanistan and Sudan, which in turn essentially moved the Taliban and Al Qaeda (which is the Taliban plus other like-minded international Islamic terrorist groups) into full Jihad against the US and its supporters. And in 2000 there was the attack on the US warship the USS Cole.
All this was the build up and eventual culmination in 9/11 attacks which had actually been planned since 1996. Unfortunately both sides are likely in a permanent stand off as the US and its allies cannot stop seeking to eradicate the terrorists, which is a tall order given it is such a loose and mobile organisation spread all over the world. And the Taliban and Al Qaeda won't stop their attacks until they're in a position where they can at least cause so much terror and fear that even global powers back down to their demands.
To this end there is no doubt that they will want to acquire nuclear or biological weapons to inflict casualties far in excess of those on 9/11, which is the really scary thing.
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