The major challenge Obama when he takes office next week faces will most likely not be Gaza, but as we suggested last Nov.6, dealing with a resurgent Russia and turning the war around in Afghanistan.

The United States has two strategic goals in Afghanistan. The first is to destroy the remnants of al Qaeda prime — the central command of al Qaeda — in Afghanistan. The second is to use Afghanistan as a base for destroying al Qaeda in Pakistan and to prevent the return of al Qaeda to Afghanistan.

From the beginning, the Karzai government has failed to take control of the countryside. Therefore, al Qaeda has had the option to redeploy into Afghanistan if it chose. It didn’t because it is risk-averse. That may seem like a strange thing to say about a group that flies planes into buildings, but what it means is that the group’s members are relatively few, so al Qaeda cannot risk operational failures. It thus keeps its powder dry and stays in hiding.

On the other hand, the United States does not control enough of Afghanistan to deny al Qaeda sanctuary, can’t control the border with Pakistan and lacks effective intelligence and troops for defeating the Taliban.

The Taliban is not inclined to make concessions to the United States because they don’t think the United States can win, and they know the United States
won’t stay.

The Petraeus/US strategy therefore is to inflict enough pain on the Taliban to cause them to rethink their position, which worked in Iraq. But it did not work in Vietnam. So long as the Taliban have resources flowing and can survive American attacks, they will calculate that they can outlast the Americans. This has been Afghan strategy for centuries, and it worked against the British and Russians.

If it works against the Americans, too, splitting the al Qaeda strategy from the Taliban strategy will be the inevitable outcome for the United States. In that case, the CIA will become the critical war fighter in the theater, while conventional forces will be withdrawn. It follows that Obama will need to think carefully about his approach to intelligence.

This is not an argument that al Qaeda is no longer a threat, although the threat appears diminished. Nor is it an argument that dealing with terrorism in Afghanistan and Pakistan is not a priority. Instead, it is an argument that the defeat of the Taliban under rationally anticipated circumstances is unlikely and that a negotiated settlement in Afghanistan will be much more difficult and unlikely than the settlement was in Iraq — but that even so, a robust effort against Islamist terror groups must continue regardless of the outcome of the war with the Taliban.

Therefore, we expect that the United States will separate the two conflicts in response to these realities. This will mean that containing terrorists will not be dependent on defeating or holding out against the Taliban, holding Afghanistan’s cities, or preserving the Karzai regime.

In due course, the counterterrorist portion will diverge from the counter-Taliban portion. The counterterrorist portion will be maintained as an intense covert operation, while the overt operation will wind down over time. The Taliban ruling Afghanistan is not a threat to the United States, so long as intense counterterrorist operations continue there.

With the blame cast on Pakistan, in the wake of the Mumbai attacks, India prepared for military action. At that point, Pakistan’s best hope was to pressure the United States into holding India back, which it did by reminding Washington of the risk it would incur to its supply lines in Pakistan – which are critical to fighting the war in Afghanistan — if the Pakistanis were faced with the need to confront a military threat from India.

Apart from the direct impact this kind of Pakistani troop withdrawal would have on cross-border operations by the Taliban, such a move also would dramatically increase the vulnerability of NATO supply lines through Pakistan. Some supplies could be shipped in by aircraft, but the vast bulk of supplies — petroleum, ammunition, etc. — must come in via surface transit, either by truck, rail or ship. Western operations in Afghanistan simply cannot be supplied from the air alone. A cutoff of the supply lines across Pakistan would thus leave U.S. troops in Afghanistan in crisis. Because Washington can’t predict or control the future actions of Pakistan, of India or of terrorists, the United States must find an alternative to the routes through Pakistan.
When we look at a map, the two routes through Pakistan from Karachi are clearly the most logical to use. If those were closed — or even meaningfully degraded — the only other viable routes would be through the former Soviet Union.

Many of the details still need to be worked out. But they are largely variations on the two main themes of either crossing the Caspian or transiting Russian territory above it.

Though the first route is already partially established for fuel, it is not clear how much additional capacity exists. To complicate matters further, Turkmen acquiescence is unlikely without Russian authorization, and Armenia remains strongly loyal to Moscow as well. While the current Georgian government might leap at the chance, the issue is obviously an extremely sensitive one for Moscow. (And with Russian forces positioned in Azerbaijan and the Georgian breakaway regions of Abkhazia and South Ossetia, Moscow has troops looming over both sides of the vulnerable route across Georgia.) The second option would require crossing Russian territory itself, with a number of options — from connecting to the Black Sea to transiting either Ukraine or Belarus to Europe, or connecting to the Baltic states.

Both routes involve countries of importance to Russia where Moscow has influence, regardless of whether those countries are friendly to it. This would give Russia ample opportunity to scuttle any such supply line at multiple points for reasons wholly unrelated to Afghanistan.

If the West were to opt for the first route, the Russians almost certainly would pressure Azerbaijan and Turkmenistan not to cooperate, and Turkey would find itself in a position it doesn’t want to be in — namely, caught between the United States and Russia. The diplomatic complexities of developing these routes not only involve the individual countries included, they also inevitably lead to the question of U.S.-Russian relations.

Even without crossing Russia, both of these two main options require Russian cooperation. The United States must develop the option of an alternative supply route to Pakistan, and in doing so, it must define its relationship with Russia. Seeking to work without Russian approval of a route crossing its “near abroad” will represent a challenge to Russia. But getting Russian approval will require a U.S. accommodation with the country.

At minimum, Moscow will want a declaration that Washington will not press for the expansion of NATO to Georgia or Ukraine, or for the deployment of military forces in non-NATO states on the Russian periphery — specifically, Ukraine and Georgia. At this point, such a declaration would be symbolic, since Germany and other European countries would block expansion anyway.

The Russians might also demand some sort of guarantee that NATO and the United States not place any large military formations or build any major military facilities in the former Soviet republics (now NATO member states) of Estonia, Latvia and Lithuania. (A small rotating squadron of NATO fighters already patrols the skies over the Baltic states.) Given that there were intense anti-government riots in Latvia and Lithuania last week, the stability of these countries is in question. The Russians would certainly want to topple the pro-Western Baltic governments. And anything approaching a formal agreement between Russia and the United States on the matter could quickly destabilize the Baltics, in addition to very much weakening the NATO alliance.

Another demand the Russians probably will make — because they have in the past — is that the United States guarantee eventual withdrawal from any bases in Central Asia in return for Russian support for using those bases for the current Afghan campaign. (At present, the United States runs air logistics operations out of Manas Air Base in Kyrgyzstan.) The Russians do not want to see Central Asia become a U.S. sphere of influence as the result of an American military presence.

Other demands might relate to the proposed U.S. ballistic missile defense installations in the Czech Republic and Poland.

We expect the Russians to make variations on all these demands in exchange for cooperation in creating a supply line to Afghanistan. Simply put, the Russians will demand that the United States acknowledge a Russian sphere of influence in the former Soviet Union. The Americans will not want to concede this — or at least will want to make it implicit rather than explicit. But the Russians will want this explicit, because an explicit guarantee will create a crisis of confidence over U.S. guarantees in the countries that emerged from the Soviet Union, serving as a lever to draw these countries into the Russian orbit. U.S. acquiescence on the point potentially would have ripple effects in the rest of Europe, too.

Therefore, regardless of the global financial crisis, Obama has an immediate problem on his hands in Afghanistan. He has troops fighting there, and they must be supplied. The Pakistani supply line is no longer a sure thing. The only other options either directly challenge Russia (and ineffectively at that) or require Russian help. Russia’s price will be high, particularly because Washington’s European allies will not back a challenge to Russia in Georgia, and all options require Russian cooperation anyway. Obama’s plan to recruit the Europeans on behalf of American initiatives won’t work in this case. Obama does not want to start his administration with making a massive concession to Russia, but he cannot afford to leave U.S. forces in Afghanistan without supplies. He can hope that nothing happens in Pakistan, but that is up to the Taliban and other Islamist groups more than anyone else — and betting on their goodwill is not a good idea.

Russia thus has enough of a foothold in Afghanistan to make life more difficult for Washington should the need arise. And the last thing the United States needs right now is for a hostile power like Russia, which it will already need to rely on for alternate supply routes, to increase friction in a critical region at a time when the United States is desperately trying to reduce friction.

On Jan. 8 however, David Petraeus also hinted at a potential U.S.-Iranian cooperation over Afghanistan.

But while in Iraq it has produced progress in curtailing Shiite militias, the Iranian Revolutionary Guard Corps (IRGC) has supplied Taliban and al Qaeda militants in Afghanistan with sophisticated improvised explosive devices to use against U.S. troops.

But if, the United States (or/and NATO) could elicit Iranian cooperation on Afghanistan, they not only could cut into the insurgent supply chain, they also could get their hands on a substantial amount of useful intelligence for use in targeting key al Qaeda and Taliban members.

In addition, the United States could look to Iran as an alternate supply route to Afghanistan. The Pakistani supply routes from the port of Karachi through the Khyber Pass or Chaman into Afghanistan — while short and relatively cheap — have become increasingly unreliable, forcing the United States to look at complex alternate and/or supplementary supply routes through Central Asia and the Caucasus. But while these alternatives as we have seen two days ago, come at a high price both logistically and geopolitically. Logistically speaking, a better alternative could traverse Iran, where  supplies could be offloaded from the Iranian port of Chahbahar, transferred to trucks and transported into Afghanistan’s Nimroz province by road.

Naturally, such a route would involve a huge leap in negotiations between Iran and the West. The United States and NATO are not about to have their war efforts in Afghanistan held hostage to a hostile Iranian regime — and the Iranians indeed are expecting a number of politically contentious concessions, ranging from Iranian nuclear rights to expanded regional influence to security guarantees from the West, in return for its cooperation.

The United Kingdom, Germany and France are the largest troop-contributing NATO members to Afghanistan after the United States. These countries however have  maintained relations with the Islamic republic, and have played a role in mediating between Iran and the United States over the years. If non-U.S. NATO members with sizable military contingents in Afghanistan could open up a separate line of negotiations for an alternate route through Iran, the burden of supplying Afghanistan could be greatly eased.

Germany is the key country to watch in this dynamic. Since the Iranians have historical reasons for distrusting the British and the Russians (both of whom briefly occupied Iranian territory during World War II), Iranians commonly see Germany as the preferred European gateway to the West. Germany is Iran’s primary Western trading partner, an economic relationship that has remained robust in spite of years of increased sanctions against Iran. The Germans currently have the third-largest NATO contingent in Afghanistan (3,220 troops) after the United States and United Kingdom, and already have made deals with the Russians to ship their supplies via Russian-influenced Central Asia. If the Germans can deal with the Russians, with whom they have a highly contentious relationship, they can very well deal with the Iranians on an additional supply route. Moreover, any supplemental negotiating track between the Europeans and the Iranians could work in concert with the U.S. diplomatic strategy for Iran, thereby injecting more confidence into Iran’s relationship with the West.

Of course, a number of significant challenges remain on the path toward rapprochement. In addition to the deep-set distrust that the United States and Iran have harbored for three decades, the nuclear issue — despite widely varying estimates on its threat value — remains a key sticking point in any diplomatic arrangement. This is especially true as the United States has to balance Iran against its relationship with Israel and the surrounding Arab states, which who all want to see Iran boxed in from all sides.

Thus the diplomatic complexities of dealing with Iran cannot be underestimated, but just a year or two ago it would have seemed quite outlandish for the United States to look to the Iranians for help on Afghanistan. What needs to be remembered is that a precedent for such cooperation exists, and though it has been a bumpy ride, the Iranians and the United States are moving toward some sort of mutual understanding on Iraq. With U.S. strategic priorities soon to be shifting from Iraq to Afghanistan, Iran and the West have yet another reason to restart negotiations.

The India Card

To complicate matters then, yesterday Indian army chief Gen. Deepak Kapoor publicly raised the possibility that “Changing our strategic policy towards Kabul in terms of raising military stakes is one of the factors that is to be determined politically.”

While careful in wording his statement, Gen. Kapoor was also deliberate in his message to Pakistan: If Islamabad continues to push India through its array of Islamist militant proxies, India could end up making a strategic decision to break through a few foreign policy barriers and shoulder some of the security burden on Pakistan’s western frontier. At a time when U.S. tolerance for Pakistan is wearing dangerously thin, and when the United States and India are exploring deeper, long-term and more strategic ties, this type of adversarial encirclement is a threat that potentially could shake Pakistan to its core.

But where there is currently no indication that the discussion is near an implementation stage, the United States would probably prefer that India keep things as they are for now. But the threat of sending Indian troops to Afghanistan does a decent job in keeping Pakistan off balance, and gives the Russians a trump card to play with.

Whatever Obama is planning to do, he will have to deal with this problem fast, before Afghanistan becomes a crisis. And there are no good solutions. But unlike with the Israelis and Palestinians, Obama can’t solve this by sending a special envoy who appears to be doing something. He will have to make a very tough decision. Between the economy and this crisis, we will find out what kind of president Obama is.