Some al Qaeda left Afghanistan before 9/11

(CNN) -- "Sleeper cells" of al Qaeda members are still operating around the world six months after their brethren struck the World Trade Center and the Pentagon, according to intelligence experts.

VIDEO Watch CNN's Mike Boettcher report (March 11) Play video (QuickTime, Real or Windows Media)   EXTRA INFORMATION Map: Follow al Qaeda's trail

More than 1,000 of these virtually invisible opponents -- well-trained, well-equipped and well-motivated -- began slipping out of Afghanistan before the U.S.-led war on terror and even before the September 11 attacks.

Sources from war on terror coalition intelligence services and from a senior official in the Afghanistan army helped CNN piece together some of the routes the terrorists traveled from Afghanistan.

At least several hundred al Qaeda members slipped through the most-guarded and well-known route, heading east toward Pakistan

Many others fled through two secret back doors -- to Iran and to two Indian Ocean islands.

Iran, to the west, served mainly as a transit point. Sources said the al Qaeda entry was not condoned by the elected Iranian government but was facilitated by Iran's more radical Revolutionary Guard.

While some al Qaeda remained there, others moved on to Lebanon, where according to intelligence sources an unknown number remain in areas controlled by the Hezbollah, a group the United States has designated as a terrorist organization.

Other al Qaeda members dispersed to the east and west to destinations unknown.

To Afghanistan's south, another back door was opened in the weeks before September 11 and for a few days immediately following.

During that period, approximately 1,000 al Qaeda operatives using false identification, made their way to the tiny Indian Ocean islands of the Seychelles and the Federal Islamic Republic of the Comoros, where they again separated into smaller groups heading east and west.

One al Qaeda cell was discovered and broken up in Singapore after its surveillance video of potential U.S. targets in that country was found by U.S. forces in an abandoned house in Afghanistan.

Accused would-be suicide bomber Richard Reid apparently was foiled in mid-flight when a flight attendant said she noticed him trying to light his shoes, which were discovered to be packed with explosives.

Many more cells remain hidden, with extensive capabilities for destruction, according to terrorism analysts.

Al Qaeda's 10-volume "Encyclopedia of Jihad" taught them assassination, bombmaking and surveillance techniques.

Then there are potential weapons of mass destruction. CNN has obtained portions of a recent addition to al Qaeda's body of knowledge -- an 11th volume devoted solely to manufacturing chemical and biological weapons from ingredients readily available to the public.

More disturbing material was found in an abandoned home in Kabul, Afghanistan, used by al Qaeda's top bombmaker. It was a document titled "Super Bomb," a discussion of the process of making a nuclear device. There was no evidence anyone succeeded.

"The program appears to have existed a long time and that is one of the things that has to give you pause is that they have been thinking about this for a long time," said nuclear physicist David Albright.

The battle against al Qaeda still rages in Afghanistan, but the biggest threat may lie elsewhere with the hidden army trained, equipped and motivated by a leader who himself has disappeared, Osama Bin Laden.

His face has not been seen since his last interview, when he vowed to press his battle inside America until victory, or until death.