The lawsuit alleges that Trudeau and MacNaughton defamed Innes by accusing her and her team of "bullying and intimidating" young Liberals during the campaign for the Liberal nomination in the downtown Toronto riding of Trinity-Spadina.
The allegations have not been tested in court.
“The claim is without merit and it will be defended vigorously," Liberal Party national director Jeremy Broadhurst said in a statement Monday. "We stand behind the campaign’s decision to red light Ms. Innes’ nomination and the party has no intention of being pressured into revisiting that decision."
In March, Trudeau launched a pre-emptive strike to prevent federal Liberals from using upcoming nomination contests to resume the toxic infighting that almost destroyed the party.
His team informed Innes that she would not be allowed to run for a Liberal nomination in any riding after receiving complaints that her husband, former MP and junior cabinet minister Tony Ianno, had been using "bullying" tactics in a bid to lure supporters away from newly elected recruit Chrystia Freeland.
Barring Innes was intended to send a message to all Liberals, Ontario campaign co-chair David MacNaughton said in an March interview.
"We're not going to go back to the days of the Hatfields and McCoys in the Liberal Party."
Innes wanted to run for the Liberal nomination in Trinity-Spadina, which faced a byelection after Olivia Chow resigned to run for mayor of Toronto.
Ianno represented the riding from 1993 until he was defeated by Chow in 2006. Innes herself twice lost to Chow, in 2008 and 2011
"Derogatory remarks were made to several young, enthusiastic Liberals about one of our leading MPs. Suggestions were made to volunteers that their future in the Liberal Party would be in jeopardy if they were on the 'wrong side' in a nomination battle," MacNaughton said in an email to Innes.
"We have all seen what Liberals fighting with Liberals can do, not only to the electoral chances of our party but to its soul. Our leader has made it clear that this kind of behaviour is not acceptable to him, nor to the thousands of people who have embraced the new way of doing politics under Justin Trudeau's leadership."
Innes said the Liberal Party's leadership had told her she'd only be approved to run in a byelection if she agreed in writing to run in a pre-assigned riding in 2015.
"This seems to be at variance with the leader’s commitment to open and fair nominations. I did make it clear to party leadership, however, that I had an open mind about which riding I would run in in 2015," Innes wrote in the email.
"It was made clear to me that if I did not submit to their demands that they would still get their way. I am now incredibly saddened that those same people have now not only manufactured allegations of apparent intimidation and bullying on young volunteers by my team, but made them public," she said, referring to unelected backroom advisers.
The defamatory allegations were widely publicized in the news last month.
Innes vehemently denies the allegations levelled against her and her campaign team.
"Despite the party leadership's public attempts to destroy my reputation I have been encouraged by a number of people from different political stripes to fight against this unfair and undemocratic action," she said Monday in reference to taking legal action.
Innes has offered to settle the case in return for a public apology, a reversal of the party's decision to intervene in the riding, and donations to the Bell Kids Helpline and Equal Voice. She says Trudeau and MacNaughton have rejected her offer.
Green-light committee cracks down
Trudeau had promised open nomination meetings in every riding across the country, including his own.
But those would-be contestants must first win the approval of the party's "green-light committee," which has the power to block those who don't meet certain standards.
For instance, prospective nominees who have yet to pay off past leadership campaign debts, such as David Bertschi and George Tkach, have been warned they'll be blocked unless they can demonstrate a credible plan to retire their debts.
MacNaughton acknowledged the decision will doubtless spark criticism that Trudeau's promise to hold open nominations is hollow, that his team is showing favouritism to ensure victory for the leader's hand-picked star candidates.
Some of Trudeau's recruits, including Freeland, were showcased at the party's convention last month, prompting some grumbling that he's giving them a leg up in nomination contests.
His team countered that opening up nominations doesn't mean the leader can't promote his preferred winners, as long as the contests are run fairly.
Nor does it mean the party has to tolerate a situation in which "the candidate who is left standing is the one who can browbeat and intimidate enough people into showing up [to vote]," MacNaughton said.
Due to redistribution, Trinity-Spadina and Freeland's neighbouring riding, Toronto Centre, will become three new ridings for the 2015 general election.