The RCMP have expanded their probe into the $90,000 the prime minister's chief of staff Nigel Wright gave to Senator Mike Duffy to include the Prime Minister's Office and Conservative senators, court documents released on Wednesday show.

The Mounties allege, in court documents filed on Nov. 15, that senior staffers in Harper's office were working closely with Conservative senators to make Duffy's expenses problems go away.

The court documents reveal new information about what the prime minister may have known about Duffy's expenses and legal bills, the extent to which senior members of Harper's inner circle were involved in the alleged cover-up, and the relationship between the Conservative Party and the auditing firm of Deloitte. One Conservative staffer even tried to raise a red flag.

​​Here are five new threads revealed by the RCMP investigation into the Wright-Duffy affair:

1. 'No evidence' Harper knew of Wright-Duffy deal

The evidence assembled by the RCMP alleges that Prime Minister Stephen Harper did not know about the details of the $90,000 cheque Wright gave to Duffy, only that "the prime minister was informed by his staff that they were working on a plan to have Senator Duffy repay expenses."

Harper has consistently maintained that he was informed of his former chief of staff's decision to repay Duffy's ineligible Senate expenses on May 15 and that had he known earlier, he would not have allowed it. Harper announced Wright's resignation on May 19.

Prime Minister Stephen Harper says a new RCMP affidavit confirms he's been 'telling exactly the truth,' as the Senate spending scandal reached further into his office Wednesday. (Chris Wattie/Reuters)

RCMP Cpl. Greg Horton, in the sworn affidavit released Wednesday, said he has seen "no evidence" to suggest that Harper was involved in having Duffy's legal bills paid, "no evidence" to suggest that Harper was personally involved in the minutiae of Wright's discussions with Duffy's lawyer, and has no evidence to suggest that Harper was involved in the repayment or reimbursement of money to Duffy or his lawyer.

Harper was made aware, on Feb. 22, that "Duffy had agreed to repay the money, that he would say he had made a mistake, and that there would be consistent media lines," Wright told the RCMP.

Wright emailed Benjamin Perrin and others in the PMO to say "I do want to speak to the PM before everything is considered final." less than an hour later, Wright wrote "We are good to go from the PM..."

Cpl. Horton said Wright maintained that "he did not tell Harper of his own eventual personal decision to pay the $90,000 to Senator Duffy."

The prime minister, however, "may have been aware that the Conservative Fund would pay the cost of Senator Duffy's legal fees, as Nigel Wright referenced in an email on Feb. 22, 2013, that he wanted to speak to the prime minister before finalizing the agreement with Janice Payne [lawyer for Duffy]," Cpl. Horton said.

2. PMO 'influenced' Duffy's Senate audit report

The RCMP has expanded its investigation to include the Prime Minister's Office, the court documents filed by the RCMP on Nov. 15 show.

While the prime minister has repeatedly told the Commons that it is Duffy who is under investigation by the RCMP and not his own office, the court documents allege that half a dozen senior members of Harper's staff and Conservatives in the Senate were involved in the matter of Duffy's ineligible expenses.

Cpl. Horton, in the sworn affidavit, alleges that the senior ranks of the Prime Minister's Office directed Conservative senators to alter the final Senate audit report into Duffy's ineligible expenses. The RCMP also alleges the PMO played a role in the deal struck between Wright and Duffy to repay the $90,000.

The PMO "influenced Senators [David] Tkachuk, [Carolyn] Stewart Olsen, and [Marjory] LeBreton to change the report to reflect wording that the PMO wanted," said Cpl. Horton.

"That wording removed all criticism of Senator Duffy."

Cpl. Horton also alleges that Tkachuk was in contact with both Duffy and Wright during the audit process. The RCMP notes it was Tkachuk who headed the sub-committee which authored the Senate report into Duffy, which turned out to be amended from its original draft version to be less critical of Duffy.

3. RCMP emails involve PMO, Conservative senators

While the RCMP has asked Duffy to turn over hundreds of emails and the PMO has said it is co-operating with the Mounties, Cpl. Horton said they have narrowed 260,000 emails down to 2,600 emails they say contain "possible evidentiary value."

The RCMP notes PMO legal counsel said the prime minister had given "clear orders" for the PMO to provide "complete co-operation" with the investigation and offer any assistance or documentation requested by the RCMP.

Who's who Individuals at the centre of the emails obtained by the RCMP and the positions they held at the time: Nigel Wright, chief of staff to Prime Minister Stephen Harper Benjamin Perrin, special adviser and legal counsel to PM Chris Woodcock, director of issues management at the Prime Minister's Office David van Hemmen, executive assistant to the prime minister's chief of staff Patrick Rogers, manager of parliamentary affairs at the PMO ​Ray Novak, deputy chief of staff to the PM Andrew MacDougall, director of communications for the PMO Senator Marjory LeBreton, government leader in the Senate Senator David Tkachuk, chair of the Senate standing committee Senator Carolyn Stewart Olsen, member of the Senate standing committee Christopher Montgomery, responsible for issues management for the government in the Senate Janice Payne, lawyer for Mike Duffy Senator Mike Duffy

Wright had previously told the RCMP that he had conveyed to only four people the real source of the funds: senior PMO staffers Perrin, David van Hemmen, Chris Woodcock, and Senator Irving Gerstein.

The emails included in the court documents filed by the RCMP on Nov. 15 primarily involve those four individuals as well as three other senior members of the PMO, namely Patrick Rogers, Ray Novak, and Andrew MacDougall. The emails also involve Senators LeBreton, Tkachuk, Stewart Olsen, Christopher Montgomery, Duffy and his lawyer Janice Payne.

On May 16, the day after Harper said he was informed of Wright's decision to repay Duffy's ineligible fees using his own funds, Chris Woodcock, the director of issues management at the PMO, wrote to Duffy about a media story that had the embattled senator quoted as saying that Wright played no role in the repayment of the expenses.

Woodcock asked Duffy if the quote was taken out of context. Duffy wrote back to Woodcock saying, "Yes, Because I did not know until Ray Novak told me that Nigel [had] given the money."

Novak wrote to Woodcock, "We need to discuss this. His lying really is tiresome."

At the time, Novak was Harper's deputy chief of staff. After Harper announced Wright's resignation, Novak took Wright's place as the prime minister's current chief of staff.

4. Senator Irving Gerstein's Deloitte contact

One of the 2,600 emails the RCMP say contain "possible evidentiary value" is an email from Patrick Rogers pertaining to Deloitte's mandate from the Senate.

Rogers writes, "Senator Gerstein has just called. He agrees with our understanding of the situation and his Deloitte contact agrees. The stage we're at now is waiting for the senator's contact to get the actual Deloitte auditor on the file to agree. The senator will call back once we have Deloitte locked in."

It is unclear from that excerpt who Gerstein's contact at Deloitte is or what the Conservatives think the Deloitte auditor will agree to.

On March 21, Gerstein contacted Rogers and said that Deloitte would not be stopping the audit, and that their mandate was to determine residency, according to an interview the RCMP conducted with Wright on July 18.

In a subsequent interview with the RCMP on Sept. 16, Gerstein said he does know Michael Runia, one of the partners at Deloitte and did ask him if there was anything he could share regarding the status of their audit.

Runia advised Gerstein that he did not know anything about it, but would inquire. Gerstein told the RCMP he relayed this back to Rogers.

Runia has regularly donated to the Conservative Party over the years, according to Elections Canada records.

Deloitte told CBC News on Thursday that the forensic review of the Senate was conducted "by a team of highly professional and objective forensic accountants."

"At no time was the ethical wall breached. No information related to the audit was provided to anyone who was not entitled to receive the information," said Caitlin Stidwill, a media relations manager at Deloitte, in an email to CBC News.

5. Senator LeBreton's staffer raised red flag

It appears there was some opposition to the changes the PMO wanted to have made to the final Senate audit report into Duffy's expenses, according to Cpl. Horton.

The opposition came primarily from Chris Montgomery, an employee of the Privy Council Office who worked for Senator LeBreton on issues management for the government in the Senate, and also from the Senate Clerk.

Montgomery "insisted the Senators were compromising themselves by changing the report to meet demands by the PMO," said Cpl. Horton.

In an interview with the RCMP on Sept. 11, Montgomery said "he advised the PMO, specifically Rogers and Woodcock, that they should not be involved" in Duffy's Senate audit and reports. Montgomery told the RCMP they ignored him.

Montgomery also told the Mounties that during his seven years in the Senate, he could not recall "other times when representatives from the PMO actually attended meetings and insisted on wording of a Senate report."

LeBreton's staffer appeared to become a thorn in the PMO's side, according to one of the emails obtained by the RCMP.

During a May 8 meeting, Montgomery wanted the Senate audit report to "remain unchanged, and there was a clear disagreement on the issue."

Patrick Rogers wrote to Wright and Woodcock saying, "I am in a meeting with Montgomery, LeBreton, Sandy [Melo, staffer to LeBreton], CSO [Carolyn Stewart Olsen]. This is epic. Montgomery is the Problem."

In the end, Montgomery "relented and the changes were made," said Cpl. Horton.

Montgomery now works in the private sector.

The RCMP also interviewed the Clerk of the Senate Gary O'Brien who said that Senator Olsen "wanted the audit on Senator Duffy to be quashed." O'Brien said her "partisan behaviour" was inappropriate for a member of the sub-committee looking into Duffy's audit by Deloitte. Olsen denied those accusations.

Wright and Duffy are alleged to have committed bribery, fraud on the government, and breach of trust between February and May 2013, according to the RCMP.

The purpose of the court documents filed by the RCMP on Nov. 15 are to seek two production orders. One for "additional documents and data" about Duffy's bank transactions, and the other for email communications of senators Duffy, LeBreton, Olsen and Tkachuk.

The allegations made by the RCMP in these court documents have not been proven in court.

No charges have been laid.