Almost two weeks after Gen. Stanley McChrystal’s resignation due to his offensive statements against the U.S. Administration published in the press, it is now clear that it was just a symptom of a much deeper crisis that is being experienced by the United States in its management of the war in Afghanistan.

Some have even suggested that McChrystal’s blunder was deliberate so that he could leave the scene before he could be blamed for the failure of U.S. strategy in Afghanistan.

Casualties among U.S. troops are still on the rise and the plan to oust the Taliban from the main strongholds in southern Afghanistan is proving to be infeasible: the Marjah offensive in the Helmand province has registered only temporary successes that have not been consolidated. The planned attack on Kandahar has been put off to September and it is still meeting with opposition also inside the Afghan government.

According to some, it was inevitable that sooner or later the discontent of the military leadership with the civilian leadership in Washington would burst out. The McChrystal Affair has kindled a major debate in the United States on relations between civilian authority and the armed forces, and on the Democrats’ ability to run a military campaign.

By readily replacing Gen. McChrystal with Gen. Petraeus, the “hero” who allowed Washington to save its face in Iraq, and stating that it was just a change in players and not in the U.S. game plan in Afghanistan, President Obama seems to have quashed the debate and is trying to give the impression that there is no structural crisis in the management of the war in Afghanistan.

However, as days go by, it is becoming less and less clear whether the White House line has prevailed over the military line, and increasingly evident that the change of command in the Afghan campaign is inevitably leading to a review of the policies adopted to date.

Many analysts were aware that the war in Afghanistan was a lost one already at the time of Obama’s inauguration. However, the evolution in the crisis of how the U.S. has managed the war is all the making of the political decisions made from then on.

According to some analysts, Obama’s failure lies in the fact that he has not been able to break away completely from the culture of war promoted by the previous Republican administration.

He has disowned the war in Iraq only to state that the real “war of necessity” is the one in Afghanistan. By agreeing to revitalize the Afghan campaign to gain the full support of Washington circles for U.S. disengagement in Iraq, he has become the hostage of the Bush legacy.

Then, when defining the strategy for Afghanistan, the contrast between the vision of the Democratic leadership, embodied by the Biden plan to limit the Afghan campaign to a mere counterterrorism mission focused only on fighting al-Qaeda, and the vision of the military leadership, embodied by the McChrystal plan to adopt a far-reaching counterinsurgency strategy (COIN) without any deadline and requiring a greater engagement of forces on the ground, came to the fore.

Obama was caught by surprise by McChrystal’s move when he publicly asked for an extra 40,000 troops for the mission’s success. What followed was a compromise (and not a shared strategy) consisting in the deployment of another 30,000 men and the setting of a deadline for the start of troop withdrawal in July 2011.

This decision was rather contradictory from the very start and it did not settle the underlying tensions between Republicans and Democrats and between the White House and the military, while actually sowing the seeds for the following contrasts that have followed.

While the military leadership has played down the relevance of the July 2011 deadline stating that the start of withdrawal would depend on actual conditions on the field, Obama has staked quite a lot on it publicizing it especially within his party and with public opinion, which is becoming increasingly tired of a war that it no longer understands the reasons for.

However, in recent weeks, criticism against the President is mounting in Washington. Many say that setting a deadline for withdrawal was a serious tactical error and that the counterinsurgency strategy is bound to fail if the enemy already knows when those enforcing it will withdraw troops.

Obama, too, seems to have recently realized that placing too much importance on the July 2011 deadline has been counterproductive because it has emboldened the Taliban, demoralized the Afghans who are collaborating with the U.S. and is driving the other coalition countries to consider withdrawal.

Therefore, although he has stated that McChrystal’s replacement with Petraeus is not a change in policy, the truth is rather different and changes in strategy will be inevitable.

One of the major problems that the Americans are facing is that they are supporting a government considered illegitimate by a growing number of Afghans especially after vote rigging last year. Petraeus may therefore exert greater pressure on the Karzai government to forward reforms, fight corruption and pursue good governance.

Petraeus may then change the extremely restrictive rules of engagement adopted by Gen. McChrystal to reduce the number of civilian casualties, which, however, have led to greater exposure for U.S. troops causing greater casualties among them.

As already mentioned, the July 2011 date may become devoid of importance and the start of troop withdrawal will probably depend on the conditions on the field. The problem is that the war is not going well for the U.S. and the White House will soon have to face a conundrum: withdraw troops accepting defeat or extending further the mission, which has proven to be a complete failure hitherto.

The military and the Republicans are for the latter option because they are not willing to leave Afghanistan without being able to shout “mission accomplished”. Obama, instead, is in favor of gradual disengagement leaving the Afghans to take control over the war.

However, since the current administration has not been willing to take the responsibility for a “defeat”, the compromise that had been reached was to send enough reinforcements to force the Taliban to negotiate a deal before starting U.S. disengagement. Unfortunately, though, the time factor was crucial to the success of a similar strategy: substantial progress on the ground and particularly the prospects of a deal were needed soon, before starting a withdrawal.

Things are not going as planned. U.S. military operations are stuck, the Karzai government is not making any progress in reforms and good governance, and the Taliban do not intend to reach any deal with the U.S.

The COIN, the counterinsurgency strategy pursued by McChrystal in Afghanistan like the one used by Petraeus in Iraq, is not giving the results hoped for (to be honest, in Iraq it has just pacified the country to the point necessary to allow for U.S. disengagement, but not to solve the problems of a country still on the verge of civil war and collapse).

Military experts are warning that COIN usually takes 12-15 years to reach success. This strategy focuses on protecting the local population, which needs services and good governance to be convinced to give its support to defeating the rebels (namely the Taliban).

However, regardless of the contradictions inherent in this strategy (the difficult balance between the use of force, which inevitably hits civilians, and the use of incentives with civilians) – contradictions that according to some are intrinsic to any plan, which can ultimately be dubbed as “colonial” – this strategy could have given results if it had been implemented from the very beginning and not after nine disastrous years of war.

After all these years, the U.S., instead of being the country’s peacemaker, has become a part of the war, siding with a government supported by the warlords who once belonged to the so-called “Northern Alliance” against a movement like the Talibans’ that is rooted especially in the country’s Pashtun ethnic group.

Moreover, the Americans have actually become an integral part of the system of corruption ruling Afghanistan, and have actually become a driving force in this system. Suffice it to mention that a recent report  has stigmatized that the system of contracts for the supplies and security of the huge U.S. logistics apparatus is actually financing corrupt government officials, the warlords, and even the Taliban, with tens of millions of dollars.

The Americans are importing everything they use in Afghanistan from Pakistan and Central Asia. In Afghanistan the procurement system is based on a transportation network controlled by Afghan contractors through a system of contracts and subcontracts. Many of these contractors are warlords who charge exorbitant prices for the security of the convoys and, in turn, pay the Taliban to avoid problems.

The Americans appear to be prisoners in Afghanistan, and it is difficult that they can dictate any conditions. The latest events in the country seem even more concerning for Washington: while the U.S. military has not taken seriously the July 2011 deadline, in Afghanistan it is considered, instead, as the clear sign of the impending departure of U.S. troops.

Clear signs are showing that the country is gearing up for the post-American era. President Hamid Karzai is intensifying contacts with the Taliban, with the Haqqani network whose bases are located in Pakistani Waziristan, and with the Pakistani intelligence, hoping to carve out a future (or – according to some – at least his own safety) after U.S. withdrawal.

Afghanistan’s minorities – the Tajiks, Uzbeks and Hazara – which have hitherto supported the government, feel betrayed by Karzai’s latest moves and do not rule out the risk of a new civil war if he were to reach a power-sharing deal with the Taliban.

Pakistan hopes that the Taliban will bring Afghanistan back into its sphere of influence covering its back in its eternal feud with the neighboring Indian giant. Delhi and Teheran are hostile to the Taliban and are preparing their countermeasures, thus posing the risk of recreating the confrontation existing after Russian withdrawal from Afghanistan in 1989, when India, Iran and Russia supported the Northern Alliance against the Taliban supported by Pakistan and Saudi Arabia.

It will be very difficult for Washington to stop all this from happening. The irony of the situation is that the fates of President Obama and Gen. Petraeus, who according to some could have been Obama’s opponent in the 2012 presidential elections, are now bound together. It is unlikely that either one can fail without dragging the other along in the defeat.