By Steve Kornacki

In his Inaugural Address, President Barack Obama noted that his would be one of the rare presidencies to begin "amidst gathering clouds and raging storms."

Hillary Clinton can say the same about her tenure as secretary of state, which officially began when her former colleagues in the Senate confirmed her by a 94-2 vote on Wednesday. While she doesn't face the same pressure as her boss to produce tangible results during her first 100 days on the job, we will learn much in that time about how much power Clinton truly has within the administration - and how she plans to use that power.

Four areas in particular figure to monopolize much of Clinton's time and energy.

The first, Iraq, is the least controversial - even though, ironically enough, it's an issue that provided the crucial early grist for Obama's campaign against Clinton. Back then, it mattered very much that Clinton had voted to authorize the 2003 invasion (and only very slowly and haltingly moved away from that support) while Obama had spoken out against it.

Now, of course, there is broad consensus, in the United States and in Iraq, that it's time to wind down the mission and withdraw, or at least severely scale back, the U.S. presence in the country. On Wednesday, Obama used part of his first full day in power to fulfill his campaign pledge to meet with military leaders and to begin planning for a 16-month phased troop reduction. The wheels seem to be in motion. There won't be much of a policy role for Clinton here, but there will be when it comes to where many of those troops will next be sent.

That would be Afghanistan, identified by Obama during the campaign as the "central focus, the central front, on our battle against terrorism." He is intent on sending an additional 30,000 troops to the country, hoping to replicate the stabilizing effect of the 2007 troop escalation in Iraq. But it's not nearly that simple.

The U.S. invaded Afghanistan in late 2001 with the goal of routing the Taliban, a mission that was accomplished with relative ease. But after that quick campaign, U.S. (and NATO) troops remained, assigned only a vague peacekeeping mission. In the seven years since, the Taliban has used the occupation to slowly rebuild all around (and more recently within) Kabul, enfeebling President Hamid Karzai - who has taken to stoking anti-U.S. sentiment in order to prop up his own political standing.

Here, Clinton faces multiple challenges. A long-term vision for Afghanistan must be defined, a cooperative relationship with the country's leaders must be reestablished, and increased support from the NATO allies still supplying troops must be secured.

In her confirmation hearings, she indicated a willingness to get tough with Karzai, who was mostly coddled by the Bush administration. She branded Afghanistan a "narco-state" and said that Karzai's government was "plagued by limited capacity and widespread corruption." We will soon learn to what extent she is willing to follow through on these words.

It also appears that Richard Holbrooke, her husband's old U.N. ambassador, will serve as Obama's envoy to Afghanistan and Pakistan. Like Clinton, he has had harsh words for the Karzai government. Reports have suggested that Holbrooke would report directly to Clinton, but given his weighty resume and high profile, their working relationship will be worth watching for signs of friction.

Another top issue, not surprisingly, will be Iran and its pursuit of a nuclear weapon. Here, both Clinton and Obama have sent very mixed signals over the past year. During their primary campaign, Clinton ridiculed Obama as "naive" when he indicated a willingness to meet with Mahmoud Ahmadinejad, Iran's president. She also threatened "to totally obliterate them" if Iran launched an attack on Israel, which has been agitating for U.S. action for years. (The outgoing Bush administration actually nixed an Israeli plan for air strikes.)

But now she has adopted Obama's tune. "We are willing to lead tough and principled diplomacy with the appropriate Iranian leader at the time and place of our choosing if, and only if, it can advance the interest of the United States," she said in her confirmation hearing. What we don't know is whether Clinton or Obama or someone else will participate in talks with Iran, and which Iranians they'd be willing to talk with.

Timing is an important issue: Elections in Iran are months away, and Ahmadinejad, thanks largely to domestic mismanagement, could well lose his job - perhaps to Mohammad Khatami, who pursued a liberalization agenda when he served as president form 1997 to 2005 and who wanted to negotiate the nuclear issue and establish diplomatic relations with the United States in 2003 (the Bush administration, drunk off its initial success in Iraq, summarily refused him). Talking to an Ahmadinejad's government may be worthless; but the election of Khatami could open a host of new possibilities.

Complicating all of this is another Obama appointment that, depending on the source, may or may not be imminent: Dennis Ross as the envoy to Iran. Ross could complicate Clinton's job in two ways. He has taken a very hard line on Iran, stoking fears among Israel's supporters not just about Ahmadinejad, but about Khatami as well. Given his hawkishness, Ross could potentially undermine efforts at good-faith discussion with Iran. And if he and Clinton don't see eye-to-eye, a power struggle could quickly emerge.

And then, of course, there is the issue of Israel and Palestine. Unlike his predecessor, Obama has already thrust himself into it, making calls to the Egyptian, Palestinian Authority, and Israeli leaders on Wednesday. He and Clinton have repeatedly affirmed their support for a two-state solution, but that concept has never seemed more endangered than in the wake of Israel's massive military operation in Gaza.

One key question is whether the U.S. will pursue some kind of engagement with Hamas, which controls Gaza. Clinton, in her hearings, played it safe and said any talks would only take place after Hamas satisfied a hefty list of preconditions. But there have been reports that Obama is willing to pursue informal engagement through intelligence services. If this is true, domestic politics are at work: It's not politically realistic for Clinton or any high-profile appointee to offer anything but condemnation of Hamas, but there are signs that the group may be more flexible - more political - than is commonly portrayed. Any progress on this front likely won't involve Clinton.

And, as with Afghanistan and Iran, Clinton also seems likely to deal with a superstar envoy, with reports that Obama will tap George Mitchell for a leading role in Israel/Palestine talks. Whether it's Clinton or Mitchell taking the lead remains to be seen. And as with Iran, timing is important, too: if Israelis elect the right-wing Benjamin Netanyahu, who took pride in blowing up previous peace efforts, in their upcoming elections, Clinton's work will be that much more difficult.

Since her surprise pick, there's been plenty of debate about whether Obama chose Clinton because of domestic politics or because of foreign policy. A hundred days from now, we should have a good sense what the answer is.