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Two former top Ontario political staffers have been criminally charged with orchestrating a plan to delete government e-mails and other documents that could have shed light on the billion-dollar cancellation of two gas-fired power plants – a long-running scandal that continues to dog the governing provincial Liberal Party.

David Livingston and Laura Miller, chief of staff and deputy chief of staff, respectively, to former premier Dalton McGuinty, each face three counts: breach of trust, mischief in relation to data and misuse of a computer system to commit mischief, the Ontario Provincial Police announced Thursday. Mr. Livingston, 63, and Ms. Miller, 36, will appear at Toronto's Old City Hall court on Jan. 27. Federal prosecutors will handle the case.

The scandal has cast a pall over Mr. McGuinty's legacy and consumed much of the energy of his successor, Kathleen Wynne, who has had to manage the fallout. The charges against Mr. Livingston and Ms. Miller come at a time when the Liberals are already reeling from another criminal prosecution, as party fundraiser Gerry Lougheed faces charges related to a different scandal. The gas-plant affair also extends all the way across the country and into the inner circle of British Columbia Premier Christy Clark, for whom Ms. Miller had been working since Mr. McGuinty stepped down.

The OPP's anti-rackets branch has been investigating for 2 1/2 years, obtaining search warrants for Mr. Livingston's BlackBerry, government computer servers and the legislature building.

Mr. Livingston and Ms. Miller allegedly brought in Ms. Miller's partner, Peter Faist, to wipe clean the hard drives of computers in the premier's office shortly before Mr. McGuinty resigned in 2013. Mr. Faist, an outside IT expert without security clearance to work on government computers, was paid $10,000 from government coffers for his services. When the payment came to light last year, the Liberal Party reimbursed the treasury.

Mr. McGuinty cancelled the unpopular plants, in the Toronto suburbs of Mississauga and Oakville, ahead of the 2011 election in what was widely seen as a bid to save local Liberal candidates from defeat. The government initially said the cancellation costs would be $220-million, but the Auditor-General subsequently estimated the total at up to $1.1-billion.

An opposition-dominated legislative committee ordered the government to release internal e-mails related to the cancellations. Police allege that, even as the committee was demanding the documents, Mr. Livingston and Ms. Miller were trying to delete them. In one e-mail previously unearthed by the OPP, Mr. Livingston instructed his staff on how to "double delete" e-mails so they could not be recovered. Peter Wallace, the province's former top civil servant, told the committee that Mr. Livingston approached him to ask how to erase files from computers; Mr. Wallace said he had told Mr. Livingston he had an obligation to preserve government records.

Both Mr. Livingston and Ms. Miller vowed Thursday to fight the charges.

Fredrick Schumann, a lawyer for Mr. Livingston, said in an e-mail that his client "did nothing wrong and certainly did not break the law as alleged." Mr. Schumann said Mr. Livingston believed his actions in the premier's office were "proper and in accordance with normal practices." Mr. Livingston has co-operated with the OPP investigation, Mr. Schumann said. "We are confident that he will be vindicated."

In a blistering statement, Ms. Miller accused the OPP of having a "clear bias" against her because she complained about two of their investigators, Detective-Constable André Duval and Detective Brian Mason, to the Ontario Independent Police Review Director (OIPRD). During the investigation, the OPP had said Ms. Miller refused to co-operate by not speaking with them. Ms. Miller said this was not true. In her statement Thursday, she said the OIPRD ordered a misconduct hearing for Det. Constable Duval, and that the OPP is appealing the decision. She has hired Clayton Ruby, a high-profile Toronto human-rights lawyer who specializes in police accountability cases, to defend her.

"I have always had trust and confidence in the police," Ms. Miller said in a statement. "Today, that is not so. After formally complaining about the conduct of the OPP in the way that they acted during their investigation into document retention, I find myself being charged. Every Canadian expects and deserves impartiality and fairness in police charging decisions. I do not believe that to be the case here."

"I believe my complaint created a clear bias by the OPP against me. Officers involved in a substantiated complaint should not have been allowed to continue investigating," she added.

Ms. Miller, who spent more than a decade climbing the ranks at Queen's Park, subsequently worked on Ms. Clark's winning 2013 election campaign and became the B.C. Liberals' executive director. She has resigned that job in the face of the charges.

Ms. Clark lauded her Thursday: "In British Columbia, Laura Miller is known to her colleagues as a person of integrity and someone who has worked hard to move our party and the province forward," she said in a statement.

The OPP declined to respond to Ms. Miller's accusation. "The OPP will not comment further on matters that are considered evidentiary in nature in order to protect the integrity of the investigation and the ensuing court process," Detective Superintendent Dave Truax wrote in an e-mail.

Ms. Wynne, who has repeatedly had to deal with the blowback from the scandal since replacing Mr. McGuinty, said in an interview she had no advance knowledge that charges were coming.

"It really is not something that we're involved in," she told The Globe and Mail. "We did not have any prior notice that this was going to happen. It's the former premier's staff – the former premier is not under investigation, he hasn't been charged with anything – and his employees will now be in the courts."

Ms. Wynne said she is hoping to pivot away from the scandal and get on with running the province: "Of course, I will answer any questions I am asked about this thing that happened in the past. But really, I'm focused on what we're doing now and what we do going forward."

Mr. McGuinty has insisted he did not know about any plan to wipe computer hard drives or delete e-mails. In his recent memoir, however, he defended the practice.

"It is absolutely essential that politicians be free to kick around political ideas – good ones and bad ones, wise ones and foolish ones. They must be free to think through their decisions out loud before they make them. There was a shredding truck outside the outgoing premier's office after my party won the 2003 election. This did not strike me as untoward. I knew the civil service has a record of all the decisions made and related Cabinet minutes," he wrote in the book, Making a Difference.

On Thursday, his lawyer pointed out that police have confirmed the former premier co-operated with the investigation by sitting down for an interview.

"In June, 2014, the OPP stated that Mr. McGuinty had been co-operative in their investigation and was not the subject of their probe. Today's events again confirm there was no wrongdoing on the part of the former premier," Ronald Caza said in a statement.

The opposition said Thursday the gas-plant scandal is part of a larger aura of political cynicism underpinning the government.

"There is a shadow of scandal that surrounds the Liberal Party," Progressive Conservative finance critic Vic Fedeli said.

Just three months ago, the Liberals faced criminal proceedings in a different scandal. Mr. Lougheed was charged with unlawfully influencing or negotiating an appointment and counselling an offence not committed after he allegedly offered a government job to former Liberal candidate Andrew Olivier in exchange for dropping his bid for the party's nomination in a by-election in Sudbury.

With reports from Karen Howlett and Jane Taber