For years they were the double act at the top of al Qaeda: the charismatic Saudi who projected aloofness while he micro-managed, and his cunning but divisive Egyptian deputy, whose prolific video output made him the public face of the network in the years after 9/11.

They had forged an alliance between their two groups, and settled into a symbiotic partnership in the Jihadist melting pot of Peshawar in the late 1980s, and in the following decade the Sudan and Taliban-run Afghanistan. Those who spent time in their company say the two men were genuinely close and enjoyed an easy and often jocular repartee. When Osama bin Laden walked into a room, Ayman al Zawahiri was often at his side, deferential and courteous - a quite calculated but also genuine show of respect -- and a metaphor for his relationship with the Saudi.

For there was also fierce ambition in the Egyptian, and some different ideas about where al Qaeda's priorities should lie, which the Abbottabad documents suggest caused a number of disagreements in the years after 9/11, with implications, given Zawahiri's accession as leader, for the future course of the terrorist network.

In recent months U.S. officials have been quoted in media reports describing growing disagreements and tension between Zawahiri and bin Laden in the years before the Abbottabad raid, with bin Laden fearing becoming marginalized. That picture, if true, is not confirmed in the documents released last week, which show that just a few months before he died, bin Laden was still actively seeking Zawahiri's advice and input. Even so the few documents released so far hint the two had some differences in strategic vision, and that their interactions had become sporadic.

Sporadic Communication

There was only one possible example of direct correspondence between Zawahiri (known in al Qaeda circles as Abu Muhammad) and bin Laden in the seventeen Abbottabad letters released by West Point's Combating Terrorism Center, an apparent distance between the two which West Point researchers called "conspicuous." A U.S. official who has viewed all the unreleased documents told CNN the two were to a significant degree cut off from each other in the years bin Laden resided at Abbottabad.

The West Point documents suggest the two instead sporadically kept in touch through intermediaries such as the Egyptian Mustafa Abu al Yazeed, al Qaeda's commander in the tribal areas of Pakistan up until his death in 2010 and his replacement Atiyah abd al Rahman, a senior Libyan al Qaeda operative, who took charge of the terror network's day-to-day global operations until his death three months after bin Laden in a drone strike.

This section of a May 2010 letter from bin Laden to Atiyah revealed the intermittent and indirect nature of bin Laden's communication with Zawahiri:

"Please send my regards and condolences to Sheikh Abu Muhammad [Zawahiri] and give me the news about his condition. For several months I have been sending messages to him, and Shaykh Sa'id [Yazeed] told me that he had not yet received a courier from him. It then became noticeable that he has not been heard in the media in recent times. I hope that the problem is something good. "

(Bin Laden was perhaps hopeful that Zawahiri had gone silent because a terrorist attack was being hatched).

Taken as a whole the new letters suggest bin Laden, who had previously played the role of chief executive in al Qaeda, was cast in the role of a meddling chairman, micro-managing and second guessing al Yazeed and al Atiyah's decision making from afar, while Zawahiri was cast into the role of a senior board member, providing advice and input into the terror network's decision-making whenever he could get messages through to the operational commanders.

It was advice bin Laden appeared to still welcome. In the fall of 2010 bin Laden sought Zawahiri's input in a letter he was drafting to send to Nasir al Wuhayshi, the leader of the group's Yemeni affiliate al Qaeda in the Arabian Peninsula (AQAP). In October he wrote to Atiyah:

"If you or Shaykh Abu Muhammad [Zawahiri] have comments on any of the paragraphs, you can delete these paragraphs and send the letter to brother Basir [Wuhayshi]. If you did not get anything from Abu Muhammad due to the difficulty in communicating between you two, and if you do not have any important comments, then go ahead and send it to Basir."

Atiyah in a June 2009 letter addressed to what West Point researchers believe was likely bin Laden wrote:

"I did send to Abu Muhammad your forthcoming project about the economic crisis, and he responded by sending a few remarks, and I did see in his remarks plenty of similarities, including removing a few statements which he saw as unsuitable."

Differences and Disagreements

Zawahiri, while deferential in his public statements, in internal correspondence made clear he did not agree with all of bin Laden's decisions. According to the Washington Post he pushed back against bin Laden's obsession with attacking the United States homeland, arguing that it would be more effective for al Qaeda to concentrate its fire on American targets in Afghanistan and Iraq. This message was not included in the recently released letters.

Zawahiri also appears to have differed with bin Laden when it came to the Somali militant group al Shabaab joining al Qaeda.

This disagreement was expressed in a letter sent to bin Laden dated December 2010 which West Point researchers believe may have been sent by Zawahiri. Its tone suggested it was authored by someone who was a close peer and confidante of al Qaeda's leader.

The letter was critical of bin Laden's decision to rebuff entreaties by the Somali militant group al Shabaab to join the al Qaeda terrorist network.

"I see it to be very essential for al Qaeda to confirm and declare its linkage with its branches...please reconsider your opinion not to declare the accession of the brothers of Somalia," stated the letter.

In an August 2010 letter to Abu al Zubayr, the commander of al Shabaab, bin Laden had written that a merger would see the "enemies escalate their anger and mobilize against you: this is what happened to the brothers in Iraq or Algeria."

After Zawahiri took over the al Qaeda leadership he soon reversed bin Laden's policy on Somalia, welcoming al Shabaab into the al Qaeda fold last February, as part of what appears to be a big tent strategy by the Egyptian to create a more cohesive organizational structure with al Qaeda "Central" in Pakistan as the center pole. During the mid 2000s Zawahiri had played a key role in negotiating affiliate status for several Jihadist groups, including al Qaeda's North African affiliate al Qaeda in the Islamic Maghreb [AQIM].

Bin Laden's letters suggested he also wanted to bring the affiliates more under the control of al Qaeda's senior leadership in Pakistan, but was more cautious than the Egyptian in granting affiliate status to Jihadist groups seeking it.

Researchers at West Point's Combating Terrorism Center who reviewed the documents wrote that bin Laden's caution on granting affiliate status brought up the possibility that Zawahiri granted such status to groups in the 2000s without bin Laden's approval.