The sudden resignation Tuesday morning of Al Jazeera director-general Wadah Khanfar sent shockwaves through the Arab media world, leading to intense speculation about whether the relative freedom the satellite network had enjoyed is about to come to an end.

In his 8 years at the helm of the network, Khanfar built it into a news powerhouse in the Middle East and beyond, angering the United States and nearly every Arab regime and -- arguably -- helping take a few of them down. He presided over the opening of Al Jazeera English, the widely praised international spinoff, which recently pried open the U.S. cable market after years of a de facto boycott. Al Jazeera's Arabic-language reporters, in particular, have taken bold risks to report the news, and not only during the Arab Spring. Some of them have paid with their lives.

Khanfar is at the top of his game. So why did he resign? In his departing note to staff, he said only that it was because he had "decided to move on" and that he had been discussing his "desire to step down" for some time.

"Upon my appointment," he wrote, "the Chairman and I set a goal to establish Al Jazeera as global media leader and we have agreed that this target has been met and that the organization is in a healthy position."

But is that the whole story? A couple theories are making the rounds, none of which seem to be based on any inside information. So what follows is purely speculative.

One potential clue is Khanfar's replacement: Ahmed bin Jassim Al Thani, a member of the royal family. Al Thani is not a journalist; he is an executive at QatarGas, a state-affiliated natural gas producer. Given that the chairman is Hamad bin Thamer Al Thani, another royal family member, this may not ultimately be such a big deal. But the optics certainly don't look good.

There were already strong reasons to question just how much editorial independence the network really has. The U.S. State Department clearly views Al Jazeera as a tool of Qatar's foreign policy; one cable from November 2009 claims that the Persian Gulf state uses the channel "as a bargaining tool to repair relationships with other countries, particularly those soured by al-Jazeera's broadcasts, including the United States." Al Jazeera devotes suspiciously little time to covering the politics of the Gulf; for instance, after Qatar's rapprochement with Saudi Arabia, criticism of the Saudi royal family dropped dramatically.

In recent weeks, the details of conversations between U.S. officials and Al Jazeera executives, including Khanfar, had been the subject of much chatter in the Arab world (Omar Chatriwala details that story for FP here). One October 2005 cable describes U.S. officials presenting Khanfar with the findings of a Defense Intelligence Agency report complaining about the network's coverage, and him agreeing to remove a particularly inflammatory slideshow from Al Jazeera's website. The cable was taken out of context and seized upon by the network's critics as evidence of a CIA-Qatari conspiracy to manipulate Arabs in the service of U.S. foreign-policy goals.

Middle East Online is running with the headline "WikiLeaks topples Al Jazeera director." But if Khanfar somehow had to resign because of the cable controversy, which has hurt Al Jazeera's credibility in certain quarters, it doesn't wash that his replacement would be a member of the Qatari royal family. Middle East Online also reports that unnamed Qatari officials were already looking to cashier Khanfar over a supposed dispute with Azmi Bishara, a Palestinian intellectual and former Knesset member who lives in Doha (and appears frequently on Al Jazeera).

So perhaps something else is going on. My sense from watching the Arabic network's coverage over the past few months is that it had more or less dropped the pretense of independence, and at times seemed like the official network of the Qatari Foreign Ministry. For instance, its Libya coverage was utterly over-the-top, enthusiastic cheerleading for the rebels -- and it just so happened that Qatar was heavily engaged in overthrowing Muammar al-Qaddafi. When Qatar brokered a peace agreement between warring factions in Darfur, Al Jazeera broke away from its normal coverage for two hours to show the final announcement. And, as many have noted, the Arabic channel's usual aggression has been noticeably lacking when it comes to Bahrain.

It's hard to imagine a hard-charging guy like Khanfar -- who clearly has his own ideological leanings -- putting up with that sort of thing for very long. So maybe he just didn't want to toe anybody's line. Whatever the reason, Arabs will be watching closely to see if his successor clips Al Jazeera's wings.

Correction: Ahmed bin Jassim Al Thani is not a former minister of commerce, as I originally wrote. And QatarGas is technically state-affiliated but not state-owned.