The project was approved by Bush, Rice, and Elliott Abrams, the hawkish deputy national security adviser.
The 2006 election result was seen as an affront to the central premise of the Bush administration's policy in the Middle East - that democratic elections would inexorably lead to pro-western governments.
With the victory of Hamas, Rice moved swiftly to try to persuade Abbas to take steps to dissolve the Hamas authority in Gaza. When Abbas did not move quickly enough, the US consul general in Jerusalem, Jake Walles, was despatched to Ramallah to deliver a curt reminder.
The magazine quotes a memo for Walles's meeting with Hamas as saying: "You should make clear your intention to declare a state of emergency and form an emergency government."
The central man figure in Washington's plan was Mohammed Dahlan, who had been Yasser Arafat's security chief in Gaza and who had established close ties with the CIA as early as the 1990s. The magazine cites three unidentified US officials quoting Bush as saying: "He's our guy."
According to the magazine, Rice played a main role in trying to persuade Egypt, Jordan, Saudi Arabia and the United Arab Emirates to offer training and funding to the Fatah fighters. Israeli officials admitted in December 2006 that Egypt had sent weapons to the Fatah faction in Gaza.
The US effort did not end with the establishment of a Palestinian national unity government. Vanity Fair describes the administration's plan B, which called for adding 4,700 new Fatah troops with additional training in Jordan and Egypt.
A state department memo put the cost for salaries, training and weapons at $1.27bn (£640m) over five years.