A recent article of the Jamestown Foundation is of great interest. Below is the web address and I have also quoted some paragraphs, though the whole article is well worth reading.
I would have to say, however, that the Jamestown Foundation is coming at the main story sideways here. Of course, any astute observer realizes, as the Jamestown Foundation points out, that the Russians run the Chechyn terror operation. What terrorist group goes out of their way to make it special point to target schoolchildren? (I have to admit that I'm not sure of Hamma's record in this regard. They obviously are happy to kill any Jews in Israel, but I don't think schoolkids are a special focus. The Cheycyns have had a relatively small # of major, headline grabbing terror operations and they choose a school for one of the targets. It is obvious nonsense. Don't forget, the men who run Russia today used to run the KGB.)
But this is beside the main point illustrated by the article, it seems to me. One implication of the article is that the Russians captured Zawahiri and "turned him." That is to say, made him into an agent of theirs, inside al Quaeda. If al Queda really was independent of Russia, and Zawhiri was functioning as a Russian agent, and it was this obvious, wouldn't al Queda kill him?
I have a much more plausible explanation for the facts cited in the article. Al Queda is controlled by the Russian KGB (which, though formally replaced by the FSB (international, ala CIA) and SVB (national ala FBI) is still operational as an "informal grouping," both running Russia and running the most sensitive of their old agents.) Zawhiri was picked up, not to "turn him," but to communicate with him on an extended basis, so he could transfer his detailed understanding of the KGB world strategy, as understood at that time, to the rest of the al Queda leadership. The reason for such indirect communications is security. If Russia does run al Queda, communications must be extremely covert. In fact, the number of contacts would have to be limited to make sure the US did not find the links. But control requires some links. This method, aresting someone, is a classic method of covert communciation.
A RUSSIAN AGENT AT THE RIGHT HAND OF BIN LADEN?
By Evgenii Novikov
Dr. Novikov is a senior fellow at the Jamestown Foundation.
"The Arabic television channel Al Jazeera broadcast an audiotape on December 19, 2003, that was said to be from Dr. Ayman al-Zawahiri, the right hand man of al Qaeda leader Osama bin Laden. In it, Zawahiri claimed that his group was chasing Americans everywhere, including in the United States. This claim helped raise the terror threat level.
But where is Zawahiri, whose head now carries a price of US$25 million? Recent media reports have said that he is hiding in Iran, though Iranian authorities deny this. Yet it could be that Russian intelligence knows exactly where he is and may even have regular contact with the elusive Egyptian.
There are many accounts of Ayman al-Zawahiri published in the press. These stories cover Zawahiri's childhood and his relatives, his study of medicine, his connections to the Muslim Brotherhood, his involvement in the assassination of Egyptian President Anwar Sadat, his close relations with Osama bin Laden, and his role in major terrorist attacks against the United States. But there are few authors who mention that Zawahiri spent half a year in close contact with representatives of Russian intelligence while in their custody.
Significantly, these contacts led to a change in Zawahiri's political orientation. Long talks with Russian intelligence officers 'forced a critical change in his lethal planning. ...America, not Egypt, became the target... Freed from Russian jail in May 1997, Dr. Zawahri found refuge in Afghanistan, yoking his fortunes to Mr. bin Laden. [Zawahiri's group] Egyptian Jihad, previously devoted to the narrow purpose of toppling secular rule in Egypt, became instead the biggest component of al Qaeda and a major agent of a global war against America. Dr. Zawahri became Mr. bin Laden's closest confidant and talent scout.' "
"...It is notable that Taliban and al Qaeda militants in Afghanistan received regular re-supplies of Russian arms. The man responsible for these deliveries was Victor Anatolievich Bout, the son of a top KGB officer. His father's connections helped establish Bout in the arms trade, which is linked to the Russian government and particularly to its intelligence services. Bout and his family currently reside in the United Arab Emirates. 
It is also not difficult to imagine that the Russians managed to get some information from Zawahiri about his colleagues that could have been used to blackmail him if he tried to avoid cooperation after his release. With an agreement reached between Zawahiri and the Russians, the authoritie