One day after he was sworn in as president of the United States and in the same week signing executive orders ushering in a new era of government transparency, Barack Obama’s Justice Department quietly filed a motion in federal court to dismiss a long-running lawsuit that sought to force the Bush administration to recover as many as 15 million missing White House emails.

In a legal briefs filed Jan. 21, the Justice Department admitted that a secretive restoration process implemented during George W. Bush’s last months in office was still incomplete, and that a bulk of the emails sent between 2003 and 2005 were deleted from servers in the Executive Office of the president and unrecoverable. The missing emails cover a time frame that included the lead up to the Iraq war, a lawsuit involving the identities of individuals and corporations who advised Dick Cheney on energy policy and the leak by White House officials of covert CIA operative Valerie Plame’s identity.

But despite it all, the newly minted Obama administration said in court papers that the issue revolving around the missing emails is “moot” because some steps, however incomplete, had been taken by the Bush White House to preserve and restore missing emails, even though the work has been conducted under the cover of secrecy by an unknown outside contractor hired by Bush administration officials.

Now, one month after the Justice Department filed its motion to dismiss the lawsuit, the plaintiffs in the case, watchdog group Citizens for Responsibility and Ethics in Washington (CREW) and the National Security Archive, the historical project that operates out of George Washington University, have filed their responses to the Justice Department with a district court judge. CREW and the National Security Archive sued the Bush administration two years ago alleging the White House violated the Presidential Records Act and Federal Records Act by not properly archiving emails from 2003 to 2005.

CREW said the Justice Department’s motion to dismiss the lawsuit “is yet another gambit in a series of actions designed to avoid transparency and accountability by obscuring the fact the Bush White House did nothing for years about a serious email problem that left a gaping hole in our nation’s history.”

The group said because there has not been an accurate and truthful accounting of how the emails went missing in the first place, “we have no assurance the problem will not be repeated.”

“With the recovery process far from complete, defendants want to go no further,” CREW said in court papers filed Friday. “But the claims in this case are not moot, requiring the court to deny defendants’ motion to dismiss.”

Further, “defendants have cast themselves as the proverbial fox guarding the henhouse door and argue in essence no outside involvement by [National Archives and Records Administration] or the attorney general is necessary because the White House -- the very entity that created the problem in the first place -- is comfortable with its analysis of and remedy for the missing email problem.”

In a sharply worded response to the position taken by Obama’s Justice Department, Archive director Tom Balnton said, “President Obama on Day One ordered the government to become more transparent, but the Justice Department apparently never got the message, and that same day tried to dismiss the very litigation that has brought some accountability to the White House email system.”

“Justice could have pulled back from that first misstep but they have not,” Blanton added. “The White House email presents a high-level test of the new Obama openness policies, and, so far, the grade is at best an incomplete.”

In a 46-page opposition to the Justice Department’s motion to dismiss filed Friday, the National Security Archive said that “as a matter of law, this issue must be resolved on the basis of a full record through summary judgment or a trial on the merits.”

“Defendants’ Second Motion to Dismiss is a last-ditch attempt to keep the facts of this case from seeing the light of day,” the Archive’s court filing says. “This court has held that the Archive’s Complaint adequately alleges that records are at risk of destruction. The Archive is entitled to develop these allegations and, if it wins on the merits, is entitled to judicial relief compelling the agency action that to this day is still withheld: referral of this matter to the Attorney General.”

In its motion filed Friday, the Archive said the White House “inexplicably selected for restoration emails from only a portion of the days that they themselves acknowledge have deleted emails; the White House did not conduct an analysis or restoration for the entire period during which emails are alleged to have been deleted; the White House excluded key periods from their analysis and restoration effort allegedly because of the migration from Lotus Notes to Microsoft Exchange; the White House relied on a statistical analysis for its estimation of whether emails were missing that used as a starting point, the quantity of email on the very servers that the White House now acknowledges were incomplete; and the White House has provided no evidence that any of the problems that led to the loss, mislabeling, and misallocation of emails have been corrected.

Six days before Obama’s Justice Department filed a motion to dismiss the lawsuit, Helen Hong, a DOJ attorney, told a federal judge presiding over the case that the White House spent $10 million to locate the emails. She claimed the emails would be transferred to the National Archives and Records Administration, along with 300 million of other documents in accordance with the Presidential Records Act, immediately after President George W. Bush left office. As such, Hong asked the court to dismiss the case.

Hong’s disclosure was made hours after U.S. District Court Judge Henry Kennedy granted an emergency order to the National Security Archive that directed Bush administration officials to immediately search all White House workstations “and to collect and preserve all emails sent or received between March 2003 and October 2005.”

Hong had also explained that independent contractors hired by the White House found the missing emails by looking through 60,000 disaster backup tapes.

In a mid-January court filing that sought dismissal of the lawsuit, the Justice Department claimed that the 14 million emails were never actually “missing,” rather the emails were simply unaccounted for due to a “flawed and limited” internal review by the Office of Administration in 2005. The documents were retrieved, the Justice Department claims, “through a three-phased email recovery process.”

The Justice Department offered up a highly technical explanation in its court filing on why the emails were unaccounted for during the internal review four years ago. Previously, Payton and White House press secretary Dana Perino had blamed the loss of the emails on the administration’s transition from Lotus Notes to Microsoft Outlook.

“The 2005 review attempted to identify the number of email messages archived in .PST files by various Executive Office of the President (“EOP”) components for dates ranging between January 1, 2003 and August 10, 2005, and concluded that 702 component days between January 1, 2003 and August 10, 2005 had “low” message counts in the EOP email system, including 493 component days had zero message counts,” the DOJ’s court filing says.

“The [Office of the Chief Information Officer] discovered that the counting tool used for the 2005 review had a message count limit of 32,000 email messages per day in a .PST file. But because large .PST files did contain more than 32,000 messages, the tool used for the 2005 review failed to “count” those messages and attribute them to components for specific days. Moreover, the 2005 review apparently relied on the name of the .PST file to allocate all of the individual email messages contained within a file to the component named in the file.

“As a result of the technical limitations of the 2005 review, 14 million messages that existed in the EOP email system in 2005 were not counted in the 2005 review. Accordingly, the 2005 review presented inaccurate message counts, concluding that approximately 81 million messages existed in the EOP email system in 2005 when, in fact, approximately 95 million email messages were preserved in the EOP email system. Those “14 million” messages were therefore never “missing,” but simply uncounted in the 2005 review.”

Obama’s Justice Department appears to have taken the Bush administration on its word that a good faith effort has been made to restore missing emails, according to CREW’s 24-page motion arguing against having the case dismissed.

“One day after the Bush administration ended, defendants filed a motion to dismiss that reflects an incredibly cynical and narrow view of defendants’ obligations under the Federal Records Act (“FRA”),” the watchdog group’s court filing says. “According to defendants, because they have taken some action -- no matter how flawed, incomplete or limited -- the first four counts of plaintiffs’ complaints are now moot. Hiding behind technical jargon and theoretical constructs, defendants attempt to obscure three basic facts: we still do not know how many emails are missing; we still do not know the source of the problem that caused emails to be missing in the first place; and we still do not know if the problem has been fixed.

“That is because rather than measure what is missing and compare that to what they have to answer the relevant questions of which emails are missing and why, defendants adopted an approach seemingly designed exclusively to undermine the results of OA’s earlier analysis. Toward that end defendants made certain assumptions not grounded in fact, employed an abstract, highly restrictive theoretical methodology to identify missing emails while ignoring the full inventory of actual emails contained on the backup tapes, and inexplicably decided to restore missing emails from less than 50 percent of the days even the most recent analysis identified as missing significant numbers of emails. Not surprisingly, defendants have not and cannot say they now have a complete set of emails from the Bush presidency.”

Sheila Shadmand, an attorney for the Archive, said she hoped the Obama administration “would give a hard look at whether to allow the defense of the Bush administration’s loss of millions of White House emails to proceed on its current course.”

“Despite assurances by Hong that “missing” emails have been recovered, David Gewirtz, an expert on email, and the author of the book Where Have All the Emails Gone? has advised the incoming administration of President-elect Barack Obama to treat White House computers left behind “like crime scene evidence.

“What must happen is this: each computer your team finds in the White House and the [Executive Office of the president] must be treated as evidence,” Gewirtz wrote in an open letter to Obama in the magazine Outlook Power prior to Obama’s swearing in Jan. 20. “Each machine must be cataloged and then removed for forensic examination. Under no circumstances should anyone on your team boot up any of those machines or use them.”