KABUL — Gen. John R. Allen was leaving Helmand province for the last time, his jet flying high above the desert moonscape that saw a bloody American military campaign and then an unprecedented withdrawal of US troops.Allen arrived here 18 months ago, charged with two seemingly contradictory goals: to defuse an active insurgency and bring home 30,000 US soldiers and Marines. Now, after the departure of a third of his force, it’s Allen’s turn to leave Afghanistan, where he says hard-fought security gains have often failed to bring about effective governance that would ensure long-term stability."In some ways, it feels like I’m leaving family behind to an uncertain future,” he said, looking out at the rugged expanse of southern Afghanistan last week.Since 2001, there have been 11 commanders of US forces in Afghanistan, five of whom, like Allen, also commanded Nato forces. But no other general was forced to focus in equal measure on both fighting a war and withdrawing from it. That meant putting Afghan soldiers in charge of combat operations even as many observers said they were unprepared. It meant building trust with an Afghan president known for intransigence, and fighting the Taliban while support waned in the US. Those were the predictable challenges.Unexpected testsThen there were the unexpected tests: the insider attacks, the burning of Korans on a US military base, the Pentagon investigation into a trove of Allen’s e-mails for possible sexual impropriety — which cleared Allen of wrongdoing last week.As his command was buffeted, Allen impressed subordinate commanders with an ability to straddle Washington’s demands for a military endgame with Afghan demands for long-term reassurance. But he says he recognized that the US drawdown would not coincide with clear-cut victory — in many cases, security gains have only brought more questions.With 11 days left in his tour, Allen says he’s proud of the growth of the Afghan security forces and the success of Nato’s troop surge in places such as southern Helmand, where four years ago the Taliban operated freely. But if security is not accompanied by effective governance, the Taliban could return, he says, or criminal networks could corrode gains."Now what they face is an absence of governance and a desire for law enforcement and legal stability,” Allen said of civilians in parts of the country that have seen strategic gains.He has been pressing Afghan officials, including President Ha¬mid Karzai, to deliver governance in places where military gains are visible. But in many cases, patronage networks have prevailed or corrupt leaders have remained in power as public confidence diminished."General Allen works for his own country. We work for the national interests of our country,” Abdul Karim Khurram, Karzai’s chief of staff, said of Allen and Karzai’s sometimes divergent views.Agencies