Woodward said the president was told of deep problems in the US relationship with Pakistan in his very first intelligence briefing -- "a cold shower" that came just days after his triumphant victory in the 2008 presidential election.
"Imagine the high of being elected on that Tuesday and they come in two days later and say, by the way, here's -- here are the secrets, and one of the secrets is Pakistan," Woodward said. "We're attacking with a top-secret, covert operation, the safe havens in Pakistan, but Pakistan is living a lie. And this is a theme throughout the whole Obama presidency: 'How do you get control of Pakistan?' "
Potentially more troubling to the administration is the revelation that, according to US intelligence reports, Afghan President Hamid Karzai has been diagnosed as manic-depressive, and is described as being "off his meds," Woodward's book reports.
"The intel agencies believe it at the highest level, and with the most graphic detail. And the intelligence shows that sometimes he's delusional, sometimes, as our ambassador [Karl Eikenberry] reports to Joe Biden last spring, 'Karzai's [sometimes] on his meds, off his meds,'" Woodward said in the interview.
Across the border in Pakistan, Prime Minister Asif Ali Zardari is depicted as quietly providing help to U.S. enemies, with the CIA suspecting that its intelligence was compromised by his government.
"You can't keep playing one side against the other," Biden warns Zardari, according to Woodward's book.
For his part, Zardari expresses frustration that Americans are too concerned about civilian casualties. Woodward reports that Zardari told then-CIA Director Michael Hayden that his poll numbers were high enough to weather blowback from casualties.
"Collateral damage worries you Americans. It does not worry me," Zardari told Hayden, Woodward writes.
Obama and his aides were also frustrated to learn that the Bush administration had let its planning for potential hotspots such as Yemen, Somalia, and Iran -- not to mention strategy in Afghanistan -- fall into disrepair, Woodward reports.
"One of the real surprises is that the Obama people found that President Bush lost his appetite for contingency planning," he said.
After he took office and commenced the Afghanistan review, Obama himself grew frustrated by the fact that military leaders kept trying to push him in a direction of providing more troops, with a looser timeframe for withdrawal.
"At one of the meetings … he just says, 'I'm pissed,' " Woodward said. "And he is, because they keep coming back about details. And they're trying to push him in that direction, and he's pushing back."
Among the other major revelations:
The US government has developed a new technology that allows for far more eavesdropping on enemy communications than has previously been known publicly. Called RTRG – Real-Time, Regional Gateway -- the system allows the National Security Agency to monitor phone calls, text messages, and e-mails constantly and has brought immediate responses by U.S. forces.
Hillary Clinton consulted longtime campaign guru Mark Penn before accepting the job as Obama's secretary of state. Penn ticked off the political benefits for her accepting, and suggested that she might replace Biden on the ticket with Obama in 2012, or run in her own right in 2016, when she'd still be younger than Ronald Reagan was when he ran for president in 1980, Woodward reports.