WASHINGTON (CNN) -- Since 2006, he has garnered an image of fixing problems at the Pentagon -- he was the anti-Rumsfeld, and his time was to be short.
Secretary of Defense Robert Gates speaks after a tour at Fort Bragg, North Carolina, on October 23.
But Defense Secretary Robert Gates now faces a host of issues he thought he would be leaving behind as the new administration prepares to move in and he stays on.
At a Pentagon briefing Tuesday, Gates summed up what he had to look forward to.
"I have no intention of being a caretaker secretary," he said. "Our challenges -- from the budget to acquisition and procurement reform, war strategy, care of wounded warriors, meeting the needs of war fighters, decisions on important modernization and capitalization projects and more -- all demand the personal attention of the secretary of defense, and they will get it."
That is heavy lifting for somebody who has said his new time as secretary of defense will be "open-ended."
Expectedly, all eyes will be on how Gates and President-elect Barack Obama will work together on troop decisions for Iraq.
For months during the presidential campaign, Pentagon officials would scoff at the idea by Democrats of a specifically timed troop withdrawal from Iraq.
After the election, the tone out of Pentagon officials seemed to change as a Status of Forces Agreement with the Iraqi government said all U.S. troops would be out of Iraq by 2011, putting the Pentagon somewhat in line with the Obama plan.
On Tuesday, Gates seemed to show support, with a caveat, for the president-elect's plan when questioned by reporters on whether he would be at odds with Obama's 16-month withdrawal plan.
"He (Obama) repeated his desire to try and get our combat forces out within 16 months. But he also said that he wanted to have a responsible drawdown. And he also said that he was prepared to listen to his commanders. So I think that that's exactly the position the president-elect should be in," Gates said. Watch Gates discuss Iraq strategy »
Afghanistan, however, will be a different story. During the campaign, Obama accused the Bush administration of forgetting about the war and pledged to put his focus there.
As NATO refuses to add more troops and the Taliban gain more strength militarily and politically around the country, a plan by Gates to rescue that military campaign was put into place -- a plan the president-elect will have to review.
"One of the first priorities of the administration will be to look at our strategy and approach in Afghanistan ... but as the president-elect has made clear, it's a very high priority," Gates said Tuesday.
The plan calls for four combat brigades, or about 20,000 troops, to be flown into the country by the end of 2009; talks between Afghan tribal leaders and reconcilable members of the Taliban; and better cooperation and support for Pakistan, where many of the fighters who enter Afghanistan come from.
For months the Pentagon has been working on the upcoming budget for the transition time. Just days after Obama is sworn in, he has to present his budget to Congress.
Pentagon officials have been planning for everything the new president will need to keep funding levels current.
Pentagon officials told CNN this month the baseline budget request for the Pentagon would be $524 billion, $9 billion more than last year, and that does not include the emergency supplemental for the wars in Iraq and Afghanistan worth billions more.
In reality, Gates will be facing numerous budget cuts in defense spending as the belt tightens for the Pentagon for the first time in eight years.
With deputies chosen by the new president, Gates could have a hard time keeping strong funding for major programs he backs, such as National Missile Defense, from the budget ax under Obama.
Obama has said he wants to dramatically cut back funding to the program, a major Bush administration focal point that came to life in his tenure.
Gates' reputation as a fixer was cemented early in his tenure when he approved the resignation of the Army surgeon general after the fallout of the Walter Reed scandal in March 2007.
Similar moves in influencing the removal of both the Air Force secretary and chief of staff after the service's nuclear weapons program was found to be in disarray proved Gates had no problem cleaning up messes.
His problem now is that he punted some messes to the next administration and now finds himself fielding those punts.
One example is the ongoing saga of the Air Force's replacement tanker program.
In September, Gates halted a broken acquisition competition that has delayed the service from getting new refueling aircraft for decades, leaving it for the next administration to handle.
As resources focused on the war on terror over the past eight years, little was done to watch the weapons acquisition programs.
Between 2001 and 2008, the Pentagon was allowed to spend $400 billion on weapons programs where many of the big-ticket items were a bust, according to industry analysts.
The list is long, from the bungled Air Force tanker to the new presidential helicopter program to the Navy's latest high-tech ships. Almost every major acquisition program is plagued by cost overruns and poor performance, senior Pentagon correspondent Jamie McIntyre reported this month.
"The key is to figure out a way to make the system work better. And I think that will be a high priority," Gates said Tuesday.
The job might not be as hard as he thinks as tightened spending for the Pentagon's budget over the coming years will play a heavy role in cutting the fat and streamlining new and existing weapons program purchases.
Gates recognizes his place in history as the only current secretary of defense to be asked to stay by a new administration. At the same time, he also will have to pay attention to his effectiveness as he will eventually find himself surrounded by staffers not totally in line with him.
He did not want to stay on, he admits, but could not say no to a man elected by the people to be president.
But with an open-ended time line for his departure, he has gotten rid of enough people to know when it's his own time to go.
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