By Frank Gardner
BBC security correspondent
There are at least 680 people being held at Guantanamo Bay
The war on terror, launched by President George W Bush and supported with vigour by Prime Minister Tony Blair, is now well into its second year.
Attacks on westerners have continued, although nothing like on the scale of those of 11 September.
So how is the war being fought and how is al-Qaeda adapting to the new realities after losing its bases in Afghanistan?
In November last year, the CIA took the war on terror to its enemies.
High above the Yemeni desert, one of its unmanned Predator drone aircraft fired a missile at a lone car, carrying six al-Qaeda suspects.
All died. They had been tracked from their base by a Yemeni informant, who phoned in their location to a joint US-Yemeni command centre.
This was the first targeted assassination by US forces outside Afghanistan.
In the fight against al-Qaeda, the rules of the game had changed.
Not far off the Yemeni coast, a hi-tech US warship is keeping constant watch over six countries around the Horn of Africa.
From Yemen to Kenya, its analysts are collating information on suspect ships, smugglers, and arms traders - anyone, in fact, who could help al-Qaeda establish a firm base in east Africa.
Earlier this year, the man in charge, Marine Corps Major-General John Sattler, told me he was getting good co-operation from the countries in the region.
"What we're looking to do is to work military to military, to train side by side, to enhance both of our forces to work in the tactics, techniques and procedures of combating terrorism.
"The other key part is the sharing of the information and intelligence."
Ready for attack
The Pentagon's Combined Joint Task Force in the Horn of Africa keeps a fleet of blacked-out helicopters for Special Operations on permanent standby in Djibouti.
They are on a moment's notice to go into action if they get hard intelligence about an al-Qaeda presence there.
The Pentagon has a similar capability at its airbase at Bagram, in Afghanistan.
MJ Gohel, from the Asia Pacific Foundation, says that since the attacks of 11 September, this ability to react quickly is needed to keep al-Qaeda on the defensive.
"The main thing is to keep hounding and harassing the al-Qaeda movement, and the idea is, if they are kept on the move they will have less time to plan attacks or to organise attacks and to recruit personnel.
"Its members are in many, many countries and you can't just keep chasing them. Eventually, the only way to get rid of this problem is to capture them."
Behind the scenes
The overt US military presence, projected on to potential terrorist hotspots like the Horn of Africa, Afghanistan and the southern Philippines, is only one aspect of the way the war is being fought.
The real war is taking place out of sight, being waged by intelligence officers, satellite analysts, translators, researchers, psychologists and interrogators.
The war on terror is primarily about trying to gather and collate intelligence.
There is now a realisation in the West that the intelligence resources it had two years ago were woefully inadequate.
Britain and the US are sharing intelligence
Since then, the CIA, the FBI, and British intelligence have all been on a major recruiting drive.
Hundreds of Arab and Asian linguists have been hired. Co-operation between agencies has improved.
Britain has set up the secretive Joint Terrorism Assessment Centre in London.
"For very many years, particularly in the US, they moved away from human intelligence and focused on technological capabilities and have paid the price for that," said Garth Whitty, from the Royal United Services Institute.
"The UK is in a much stronger position, but there is still a long way to go before we have the sort of coverage and penetration that is necessary."
But what about al-Qaeda itself, the principal target in the West's war on terror? How is it adapting to being permanently on the run?
Several times in recent months, both Osama bin Laden, his deputy Ayman Al-Zawahiri - or at least people purporting to be them - have made fiery broadcasts to their followers.
They no longer send videotapes to TV stations. It is considered to be too risky for their own safety.
But on the airwaves and on the internet, al-Qaeda's fugitive leadership has been calling on Muslims to rise up against their rulers and to attack Americans.
There have been attacks - in Bali, in Kenya, in Tunisia and Pakistan.
A former CIA operative, Mike Baker, who now runs the security company Diligence, believes al-Qaeda has effectively decentralised its operations.
"They have proven to be tactically adaptive. We have done significant damage to their financial structure, to their ability to communicate amongst themselves, and to their ability to move resources and personnel. But what they have done is to decentralise the way they do business".
What this means in practice is that small, localised groups with previously local agendas, like those in Africa and Asia, are now being encouraged by al-Qaeda to broaden their hit-list to include westerners.
MJ Gohel says we should now think of al-Qaeda, not so much as an organisation, but more as a global movement.
"In the past there were regional groups with regional aspirations, but over the last few years what has happened is they have all come under a kind of global jihad movement.
"These are people who now have agendas which go beyond their own borders. They wish to form Islamic caliphates, Islamic super-states, around the world."
The worry for the West, and for Israel, is that al-Qaeda has endless patience.
It sees 11 September as a wake-up call to Muslims after centuries of colonisation and repression.
For many, recent events in Iraq and the Palestinian territories have only confirmed those beliefs.