Citizens for Responsibility and Ethics in Washington (CREW) and the National Security Archive (NSA) sued in 2007, after it was revealed that the Bush White House had discovered in 2005 that the emails were missing, but had failed to restore them, and had knowingly continued to use a broken system for preserving electronic records.
CREW notes in a press release:
Documents produced so far show the Bush White House was lying when officials claimed no emails were ever missing. The record now proves incontrovertibly that Bush administration officials deliberately ignored the problem and, in fact, knowingly allowed it to worsen.
The Obama administration appears to have gone above and beyond. As part of the agreement, it pledged to recover presidential records that the court had ruled the plaintiffs lacked the standing to sue over. Some of those are from the office of vice President Dick Cheney, which played a key role in numerous Bush administration controversies, and developed a reputation as a particularly zealous defender of government secrecy.
Because of funding constraints, not all the emails will be restored. According to CREW, "the dates for restoration were chosen based on email volume and external events."
You can read the full agreement here (pdf).
Late Update: Sen. Pat Leahy, who had pressed the issue under the Bush administration, said in a statement:
The Senate Judiciary Committee never accepted the Bush administration's conclusion that millions of its emails were 'lost.' In fact, President Bush's spokesperson was dismissive of congressional requests that the administration recover the emails. This was another example of the Bush administration's reflexive resistance to congressional oversight and the public's right to know.