“We have slowed a primary cancer,” U.S. Defense Secretary Leon Panetta said recently, referring to Al Qaeda, “but we know that the cancer has also metastasized to other parts of the global body.” At first glance, this is simply the latest repackaging of a frequent refrain: U.S. efforts in Afghanistan have succeeded, but Al Qaeda affiliates in Yemen, Somalia, and elsewhere still pose a threat. Yet Secretary Panetta’s metaphor—Al Qaeda as cancer and America as the surgeon—actually reveals how U.S. strategy in Afghanistan went astray.

Taking the metaphor a step further, it was the prescription, not the diagnosis, that warped President Barack Obama’s “good war.” Tragically, a combination of American ambition, goodwill, and ignorance about the limits of U.S. power rejected limited intervention in favor of broader rehabilitation.

As a presidential candidate, then senator Obama made a compelling case that the Bush administration poorly triaged U.S. foreign-policy priorities, mistakenly putting Iraq ahead of Afghanistan. President Obama also accurately diagnosed the illness when announcing a new U.S. strategy for Afghanistan in March 2009: “I want the American people to understand that we have a clear and focused goal: to disrupt, dismantle, and defeat Al Qaeda in Pakistan and Afghanistan, and to prevent their return to either country in the future.”

But this clarity quickly began to cloud. America would shift its focus to training Afghan security forces, but that was not enough. President Obama added missions to “advance security, opportunity, and justice – not just in Kabul, but from the bottom up in the provinces – we need agricultural specialists and educators; engineers and lawyers.” These were noble goals, but they depended on a credible partner in the Afghan government who did not exist and couldn’t be invented. Here, the doctor overestimated his strength and underestimated the patient’s weakness.

In The Emperor of All Maladies, doctor and author Siddhartha Mukherjee describes how pioneering oncologists took increasingly severe steps to treat cancer patients in the late 19th and early 20th centuries. “Pumped up with self-confidence, bristling with conceit and hypnotized by the potency of medicine, oncologists pushed their patients—and their discipline—to the brink of disaster,” Mukherjee explains. One fallen hero is Dr. William Halsted, a leading surgeon whose gruesome radical mastectomies removed not only the breasts, but also the surrounding tissue, lymph nodes and pectoral muscles.

So it went in Afghanistan. Hypnotized by the apparent success of counterinsurgency doctrine in Iraq, U.S. officials examined the patient and prescribed wide-ranging treatment. As General Stanley McChrystal said during his Senate confirmation hearing in 2009, “Afghans face a combination of challenges . . . There is no simple answer. We must conduct a holistic counterinsurgency campaign and we must do it well.” Consequently, a more focused counterterrorism strategy, advocated by Vice President Biden and others, was jettisoned for a larger U.S. military footprint and grander goals.

Cutting too deeply, America tried to transform Afghanistan’s opium economy. The Obama administration shifted its focus from drug eradication to interdiction in 2009, but it never gave up on the fantasy of enticing Afghan farmers to grow alternative crops. The idea of fighting terrorism by planting pomegranates seemed right at home among the yin-yang dictums of counterinsurgency doctrine like “the best weapons for counterinsurgency do not fire bullets.” Yet despite receiving over $6 billion from Uncle Sam for counternarcotics efforts since 2002, Afghanistan continues to produce roughly 90 percent of the world’s opium.

Perhaps the grandest goal of all was curing Pakistan’s paranoia. While cooperating with the U.S. military in some areas, Pakistan has continued to provide safe haven for Taliban fighters and Al Qaeda operatives. In the face of Pakistan’s double game, some Western experts looked to India for solutions. The key to winning the war in Afghanistan, they argued, was brokering a peace between Pakistan and India on the status of Kashmir, a constant source of conflict since Pakistan’s independence in 1947.

Missions don’t creep with such thinking—they cascade. Indeed, both original goals seem absurd in light of today’s realities. Al Qaeda in Afghanistan and Pakistan has been decimated, but its demise had little to do with replacing opium or calming Pakistani fears. Meanwhile, Afghanistan’s political challenges—safe havens in Pakistan, corruption, drugs and poor governance—all remain.

The holistic approach has been costly, but 9/11 cautions against pulling the plug and walking away. After being bombarded with campaign rhetoric, many Americans likely believe the current plan is just that: full withdrawal of U.S. forces by the end of 2014. But as Secretary Panetta has recently reminded the public, post-2014 troop levels will be announced in the coming weeks. To prevent Afghanistan from relapsing, the United States will likely maintain a small residual force for counter-terrorism missions, intelligence collection and training Afghan forces. In short, it will prescribe the limited treatment that was never tried.

Jonathan E. Hillman is a graduate student fellow at Harvard’s Belfer Center for Science and International Affairs.