A few days before the presidential election, the leadership of the anti-Trump Lincoln Project gathered at the Utah home of Steve Schmidt, one of the group’s co-founders, and listened as he plotted out the organization’s future.

None of the dissident Republican consultants who created the Lincoln Project a year earlier had imagined how wildly successful it would be, pulling in more than $87 million in donations and producing scores of viral videos that doubled as a psy-ops campaign intended to drive President Donald J. Trump to distraction. Confident that a Biden administration was on the horizon, Mr. Schmidt, a swaggering former political adviser to John McCain and Arnold Schwarzenegger, pitched the other attendees on his post-Trump vision for the project over a breakfast of bagels and muffins. And it was ambitious.

“Five years from now, there will be a dozen billion-dollar media companies that don’t exist today,” he told the group, according to two people who attended. “I would like to build one, and would invite all of you to be part of that.”

In fact, Mr. Schmidt and the three other men who started the Lincoln Project — John Weaver, Reed Galen and Rick Wilson — had already quietly moved to set themselves up in the new enterprise, drafting and filing papers to create TLP Media in September and October, records show. Its aim was to transform the original project, a super PAC, into a far more lucrative venture under their control.

This was not the only private financial arrangement among the four men. Shortly after they created the group in late 2019, they had agreed to pay themselves millions of dollars in management fees, three people with knowledge of the deal said.

One of the people said a contract was drawn up among the four men but not signed. A spokeswoman for the Lincoln Project was broadly dismissive and said, “No such agreement exists and nothing like it was ever adopted.”

The behind-the-scenes moves by the four original founders showed that whatever their political goals, they were also privately taking steps to make money from the earliest stages, and wanted to limit the number of people who would share in the spoils. Over time, the Lincoln Project directed about $27 million — nearly a third of its total fund-raising — to Mr. Galen’s consulting firm, from which the four men were paid, according to people familiar with the arrangement.

Conceived as a full-time attack machine against Mr. Trump, the Lincoln Project’s public profile soared last year as its founders built a reputation as a creative yet ruthless band of veteran operators. They recruited like-minded colleagues, and their scathing videos brought adulation from the left and an aura of mischievous idealism for what they claimed was their mission: nothing less than to save democracy.

They also hit upon a geyser of cash, discovering that biting attacks on a uniquely polarizing president could be as profitable in the loosely regulated world of political fund-raising as Mr. Trump’s populist bravado was for his own campaign.

Then it all began to unravel. By the time of the Utah meeting, the leaders of the Lincoln Project — who had spent their careers making money from campaigns — recognized the value of their enterprise and had begun to maneuver for financial gain. But other leaders had learned of the financial arrangement among the original founders, and they were privately fuming.

Another major problem was festering: the behavior of Mr. Weaver, who for years had been harassing young men with sexually provocative messages.

Allegations about Mr. Weaver’s conduct began appearing in published reports in The American Conservative and Forensic News this winter. In late January, The New York Times reported on allegations going back several years. The Times has spoken to more than 25 people who received harassing messages, including one person who was 14 when Mr. Weaver first contacted him.

Fresh reporting by The Times found that Mr. Weaver’s inappropriate behavior was brought to the organization’s attention multiple times last year, beginning in January 2020, according to four people with direct knowledge of the complaints, though none of the warnings involved a minor. The Lincoln Project’s spokeswoman, Ryan Wiggins, said it would not comment on issues related to Mr. Weaver while an outside legal review of Mr. Weaver’s actions was ongoing. The group has hired the law firm Paul Hastings to conduct the review.

Last June, an employee for a company hired by the Lincoln Project warned in an email that Mr. Weaver’s conduct was “potentially fatal” to the organization’s image. The email, sent to a board member and circulated to other leaders, described multiple instances of harassment. It said Mr. Weaver’s behavior was already damaging relationships with vendors and offered to put leaders in contact with some of the men involved.

Over the last month, The Times reviewed documents and conducted interviews with the founders and with scores of current and former contractors, executives, interns and men who were harassed by Mr. Weaver. Some spoke on the condition of anonymity to discuss sensitive internal deliberations, and others because they feared retaliation from Lincoln Project leaders.

The crisis surrounding Mr. Weaver, and the splintering of the group’s leadership, have cast the future of the Lincoln Project into doubt. Within weeks of the meeting in Utah, a battle erupted over who would control the group’s board. There would be threats to sue, to start rival groups and to back different board slates, as millions of dollars were moved in and out of the organization.

Even people once associated with the group, including George T. Conway III, have called for its dissolution. But Mr. Schmidt’s faction intends to continue it as a modern media campaign against global forces of authoritarianism, while also monetizing the movement.

Save for Mr. Weaver, the project’s top leadership — Mr. Schmidt, Mr. Galen and Mr. Wilson — has not changed. They are hoping that enough of its more than 500,000 donors will remain to keep its coffers filled.

Mr. Schmidt, in a recent interview conducted shortly before he took a leave of absence, said this was no time to quit.

“I want the Lincoln Project to be one of the premier pro-democracy organizations,” he said. “We believe there is a real autocratic movement that is a threat to democracy and has a floor of 40 percent in the next election. And the pro-democracy side cannot be the gentle side of the debate.”

An unexpectedly fast rise

It was not initially clear that the Lincoln Project would be so wildly successful. Then, last May, it released its “Mourning in America” video, a play on a Reagan-era commercial that laid the failures of the country’s pandemic response squarely at Mr. Trump’s feet.

The commercial prompted a late-night Twitter barrage from Mr. Trump to his tens of millions of followers. He derided the project as “a group of RINO Republicans who failed badly 12 years ago, then again 8 years ago, and then got BADLY beaten by me,” adding, “They’re all LOSERS.”

Mr. Trump’s outburst gave the Lincoln Project a flood of attention it could have only hoped for. Fund-raising surged. In June, the billionaire investor Stephen Mandel donated $1 million, while Joshua Bekenstein, a co-chairman of Bain Capital, and David Geffen each donated $100,000; Mr. Geffen has since given $500,000 in total. (David Dishman, the executive director of the David Geffen Foundation, said that Mr. Geffen’s donations were “specific to their work around the 2020 election cycle.”)

It was the start of a wave of contributions, not all from financial powerhouses like Mr. Geffen. The Lincoln Project raised more than $30 million from people who gave less than $200.

A hiring spree began, and the organization spread its wings, creating a communications shop, a political division, podcasts and political shows for its website. It went from “eight or 10 people on the first of May, to like 60-plus by late or early July,” Mr. Galen said. “We scaled up enormously quickly.”

Initially, the project operated much like a pirate ship. Typical workplace management practices were lacking. The organization has no chief executive. Two of its largest contractors, who were billing the Lincoln Project, were given seats on the three-member board of directors, a breach of normal governance practices.

The executive structure was malleable: The two contractors on the board, for instance, Ron Steslow and Mike Madrid, who were each involved in reaching voters through digital advertising and data targeting, were also referred to as co-founders. So were Mr. Conway and Jennifer Horn, a former head of the Republican Party in New Hampshire who joined early on and played a leading role in outreach to independents and Republicans.

“This thing was literally a pop-up stand,” said Mr. Conway, an unpaid adviser who had no real operational role before stepping away from the organization last summer. “It was an organization that got big really fast, and more money came in than anyone could have imagined. It was just catch as catch can.”

Amid the rapid growth, it was the core group of original founders, led by Mr. Schmidt, who wielded operational control. “I had zero decision-making power,” Sarah Lenti, a Republican political consultant who at one point served as the group’s executive director, said in an interview.

Ms. Lenti, who has worked on four G.O.P. presidential campaigns in a variety of roles, added that she “was never privy to what founders were making.”

If liberals viewed the Lincoln Project’s mission as noble, the four Republicans who started it had long been practitioners of bare-knuckled political brawling.

Mr. Wilson was a longtime G.O.P. strategist known for producing jagged attack ads, like one in 2002 that claimed former Senator Max Cleland, a Georgia Democrat who had lost both legs and his right hand in Vietnam, lacked the courage to defend America against terrorists.

The other three were alumni of Mr. McCain’s presidential campaigns. Mr. Weaver is a brooding and mercurial Texan whom Mr. McCain nicknamed Sunny. Mr. Schmidt, played by Woody Harrelson in the movie “Game Change,” championed Sarah Palin as Mr. McCain’s vice-presidential nominee in 2008, a decision he later called a mistake. He and Mr. Weaver are not remembered fondly by the McCain family, judging by a recent tweet from Meghan McCain, the former senator’s daughter, who said that in recent years, “no McCain would have spit on them if they were on fire.”

Mr. Galen, once a Schmidt lieutenant and now an equal partner, said of presidential campaigns, “It’s not Montessori school.”

As money poured in, robust cost controls were lacking, with founders reaping management fees. And while big payments are common in politics, other Lincoln Project officials and employees were shocked at the scale when federal records revealed that nearly $27 million had been paid to Mr. Galen’s consulting firm, Summit Strategic Communications. It is not known how much of that each of the four received. Their private arrangement shielded even from other senior officials the size of the individual payments.

“Based on public reports, I clearly was not compensated anywhere near as lavishly as others seemingly were, earning a small fraction of what some of my male counterparts did,” Ms. Horn said in a recent statement.

Obscuring payments via intermediary firms can violate campaign finance laws, but it is unclear whether the Lincoln Project crossed that line.

Ms. Wiggins, the spokeswoman, said Summit was one of the prime contractors that managed and performed work for the Lincoln Project, citing voter outreach efforts and placing advertisements. “All prime contractors and subcontractors were paid in accordance with industry standards,” she said.

Mr. Galen was also earning commissions on nearly $13.3 million directed to another contractor, Ashton Media, which placed the group’s television ads, a former Lincoln Project official said. The project declined to discuss the commissions but said in a statement that it was “standard practice” to use “either a percentage, fixed-fee or hybrid model for media buying.”

Jan Baran, a longtime Republican campaign finance lawyer, said that it was “customary and customarily controversial” for campaign consultants to steer business to their own firms, but that, typically, candidates and PACs negotiate those fees down. What makes the Lincoln Project different, he said, is that “the consultants are their own client, so I’m guessing the negotiations wouldn’t have been as rigorous.”

Unaddressed complaints

In the midst of the Lincoln Project’s overnight success last summer, a troubling email arrived.

“I’m writing regarding a pattern of concerning behavior by Weaver that has been brought to my attention by multiple people,” it began. “In addition to being morally and potentially legally wrong, I believe what I’m going to outline poses an immediate threat to the reputation of the organization, and is potentially fatal to our public image.”

The email was sent to Mr. Steslow, the Lincoln Project contractor and board member, by an employee at his company, Tusk, which handled the project’s digital advertising. It described a wide array of allegations dating from 2014 to 2020, including what it called a “bait-and-switch situation” around 2015 in which Mr. Weaver offered to discuss a political job with a young man, then tried to bring him to his hotel room instead. It also said that Mr. Weaver had continued to harass people after the Lincoln Project was founded in late 2019, and that he had “mixed suggestive commentary with official T.L.P. marketing work.”

The Times obtained a portion of the message, and multiple people who have read it provided detailed descriptions of the rest. It included an offer to provide more information if Lincoln Project leaders requested it.

This was not the first time that allegations of harassment by Mr. Weaver had been reported to project leaders. In January, five months before the email was sent, another person working for Tusk had raised concerns with Mr. Steslow.

Ms. Lenti said she was told last March, when she was executive director, that Mr. Weaver “had a history of flirting with gentlemen over Twitter in an inappropriate fashion.”

Mr. Steslow pressed unsuccessfully for some time to have Mr. Weaver pushed out, five people with knowledge of the matter said. While he informed other Lincoln Project officials as early as February 2020 of his concerns, three of the people said, there are conflicting accounts of who learned about Mr. Weaver, what they learned and when.

Mr. Schmidt has been adamant that he had “no awareness or insinuations of any type of inappropriate behavior,” only rumors that Mr. Weaver was gay, even as concerns about harassment were percolating within the organization he was helping run. Mr. Galen was made aware of the June email, the five people with knowledge of the matter said; he declined to comment on the issue, citing the outside legal review the Lincoln Project has commissioned.

The Lincoln Project did not begin an internal review into Mr. Weaver’s conduct until after the email from the Tusk employee arrived in June. It was led by the group’s general counsel, Matt Sanderson, but was limited in scope, according to Ms. Lenti and others. Ms. Lenti said that to her knowledge, only two people who had complained about Mr. Weaver’s messages were contacted. The June email contained many more allegations that were never followed up on.

“I was not made privy to any written report, if there was ever one, and to my knowledge only the two gentlemen were interviewed,” Ms. Lenti said, adding that Mr. Weaver himself had not been interviewed.

Mr. Sanderson declined to comment, citing the legal inquiry.

By the time the Lincoln Project was founded, Mr. Weaver had been harassing young men online for years. In the most aggressive messages reviewed by The Times, he explicitly offered professional help or mentorship in exchange for sex. Other times, he asked young men about their height, weight and other measurements, and suggested they get drinks or travel together.

Mr. Weaver took a medical leave in August, quieting internal dissent. But soon afterward, he was included as an equal partner in Mr. Schmidt’s proposed private media venture. Axios reported in late October that the Lincoln Project was “weighing offers from different television studios, podcast networks and book publishers.”

That was news to Mr. Steslow, Mr. Madrid and Ms. Horn, according to three people with knowledge of the matter. It exacerbated tensions that had been simmering since the summer, when the trio had resisted a brief effort by the original founders to strip them of their titles as co-founders, the people said.

By Oct. 30, Mr. Steslow, Mr. Madrid and Ms. Horn were already on edge as they gathered at Mr. Schmidt’s Utah house, listening as he outlined his vision for a media company. And it was soon made clear to them that they would not be equal partners. Though Mr. Schmidt had already brought Mr. Weaver in on the media deal, he referred to him indirectly as a “black box” that needed to be resolved, but didn’t give details.

What Mr. Schmidt didn’t say was that the four original principals had already signed a 27-page agreement for TLP Media that named Mr. Schmidt as manager and required each to chip in $100,000 for an equal share, according to a copy reviewed by The Times.

Asked about those documents, Ms. Wiggins, the spokeswoman, said: “This is an inactive company — it only ever existed on paper, never conducted any business, and was never capitalized by its due date, making it null. There are no plans to use this business in the future.”

Game change

Not long after the election, with relationships fraying over the group’s finances, Mr. Schmidt and Mr. Wilson sought to formalize their control of the project by pushing to join the board of directors, multiple people with knowledge of the effort said. Mr. Steslow and Mr. Madrid were sent a resolution to sign that would add Mr. Schmidt and Mr. Wilson to the board. Mr. Steslow and Mr. Madrid instead requested a meeting to discuss the proposal. They were rebuffed.

A bitter standoff began. With Mr. Steslow and Mr. Madrid still in control of the board, Mr. Galen, aligned with Mr. Schmidt and Mr. Wilson, set up a new entity of their own called Lincoln Project 2024. In December, they moved millions of dollars from the existing Lincoln Project into companies they controlled, which would have left behind a hollowed-out shell, several people with knowledge of the dispute said. (Mr. Galen said, “Anything regarding this, I can’t speak to.”)

Mr. Steslow and Mr. Madrid, threatened with litigation by the original founders, asked to review the organization’s books, as well as information related to Mr. Galen’s consulting firm.

Mr. Conway tried to mediate. “I told them all these threats and counter-threats are going to blow up the organization and destroy something that had done so much good,” he said.

It was only during the course of that mediation, Mr. Conway added, that he first learned something about Mr. Weaver’s behavior. Mr. Steslow and Mr. Madrid told him they were concerned that Mr. Weaver might still be getting paid despite having sent inappropriate messages to young political consultants, Mr. Conway said, though he added that he wasn’t given details or told that it involved people who worked with the project.

In the end, the transferred funds were returned to the Lincoln Project, Mr. Schmidt and Mr. Wilson joined the board, and a settlement was reached with Mr. Steslow and Mr. Madrid, who departed in December.

Both declined to comment, citing a confidentiality agreement. While the organization has publicly offered to waive such agreements, several people with knowledge of the matter said the offers were limited.

The infighting remained largely invisible until January, when reports surfaced about Mr. Weaver’s conduct. Ms. Horn soon departed, assailing fellow leaders’ handling of the situation and saying she had only recently become aware of it. “When I spoke to one of the founders to raise my objections and concerns, I was yelled at, demeaned and lied to,” she said.

Recriminations were swift. Ms. Horn’s private Twitter messages were posted to the project’s official Twitter account, then quickly taken down, a highly unusual breach of privacy; her lawyers have given notice of a potential lawsuit.

Mr. Schmidt retreated, leaving the board he had only recently joined. He also apologized to Ms. Horn for letting “my anger turn a business dispute into a public war” and called her “an important and valuable member of our team.”

Those comments were part of a lengthy statement in which Mr. Schmidt said the Weaver episode had reawakened his anger at sexual abuse he had experienced as a boy, as he sought to explain the group’s widely criticized response.

“I am incandescently angry about it,” he said of Mr. Weaver’s actions. “I know the journey that lies ahead for every young man that trusted, feared and was abused by John Weaver.”

Rehabilitation project

As the Lincoln Project tries to reboot, in some ways little has changed. The project is still controlled by three of the four men who started it. Cognizant of a lack of diversity in the organization — all four original founders are white — they have asked Tara Setmayer, a Black senior adviser and former House Republican communications director, to lead a transition advisory committee.

Ms. Setmayer called the project a movement of people “who decided to get involved to help rehabilitate our democracy.” But from the start, it has blended money with mission. For some, like Mr. Conway, there was no money involved. For others, it was incredibly lucrative.

Few have been more omnipresent than Mr. Schmidt, who has gleefully brawled with the Trumps. Remarking on images of the family’s last Jan. 20 photo op, he tweeted, “Uday and Qusay looking sad,” conflating Donald Trump Jr. and Eric Trump with the sons of Saddam Hussein. “Crying Ivanka. Glorious indeed.”

Stuart Stevens, a longtime media consultant who has taken an increasingly prominent role in the project, cried during an interview while talking about his commitment to the cause.

“I helped create this monster that is the current Republican Party,” Mr. Stevens wrote in a follow-up email. He called the recent tumult at the Lincoln Project “a rough couple of weeks,” adding: “This isn’t supposed to be easy. We’re human. We make mistakes. There’s stress at the highest level. All you can do is acknowledge, take responsibility and move on.”

Whether donors will keep the spigot open, especially with Mr. Trump both outside the White House and off Twitter, remains to be seen.

“I’ve been talking to a lot of donors,” Mr. Stevens said. “The support is tremendous. Most of them have been involved in business and had a few rough times. They were drawn to Lincoln Project not because we were H.R. geniuses but because we knew how to fight and were willing to take on our own party. That hasn’t changed.”

But the Weaver problem will linger.

“The attacks that are coming on us from Donald Trump Jr. and all these other people, they’re gleeful — they love the gift that John Weaver gave them,” Mr. Wilson said in an emotional monologue on the group’s video program “The Breakdown” last month. “What he’s given them is a weapon in their hands.”

Shane Goldmacher contributed reporting. Kitty Bennett and Rachel Shorey contributed research.