Last year, GitHub appeared to be the perfect Silicon Valley startup. After essentially bootstrapping for four years, it accepted a $100 million investment from hot venture capital firm Andreessen Horowitz. It boasted that none of its employees had ever quit.

Now the integrity of its co-founder and another executive are being questioned by a former employee who alleges she was verbally and sexually harassed.

There are a lot of accusations flying around, and it's very complicated. But here's the crazy situation, explained.

Julie Ann Horvath, the former employee who says she was harassed.

Julie Ann Horvath About.me / Julie Ann Norvath In March 2012, Julie Ann Horvath joined GitHub as a designer. She stayed for two years, until this past March when news of her resignation broke on the anonymous gossip app Secret: "Self proclaimed queen of GitHub is leaving. The masses cheer," it read.

Secret, some people think, is what pushed her to flame the company on Twitter.

.@getsecret told me they took down a post that's attempting to assassinate my character. They didn't. It continues. pic.twitter.com/JKCHH1prC6 — Julie Ann Horvath (@nrrrdcore) March 15, 2014

After Horvath saw the Secret post, she began publicly tweeting about the reasons she quit GitHub. The tweets accused one of GitHub's co-founders, the co-founder's wife, and another GitHub employee of harassment.

Here are some of her specific claims:

She also told TechCrunch in an interview following the tweets that the wife of one of GitHub's co-founders had tried to verbally and physically intimidate her. The person she was referring to is Theresa Preston-Werner, whose husband Tom came up with GitHub in 2007. Horvath told TechCrunch's Alexia Tsotsis:

I met her [for drinks] and almost immediately the conversation that I thought was supposed to be casual turned into something very inappropriate. She began telling me about how she informs her husband’s decision-making at GitHub, how I better not leave GitHub and write something bad about them, and how she had been told by her husband that she should intervene with my relationship to be sure I was ‘made very happy’ so that I wouldn’t quit and say something nasty about her husband’s company because ‘he had worked so hard.’

Horvath also alleged that a fellow colleague, an engineer whom she says has since been promoted, treated her inappropriately.

"Horvath had what she referred to as an awkward, almost aggressive encounter with another GitHub employee, who asked himself over to 'talk,' and then professed his love, and 'hesitated' when he was asked to leave," TechCrunch reported in March.

"Hurt from my rejection, [he] started passive-aggressively ripping out my code from projects we had worked on together without so much as a ping or a comment," Horvath told TechCrunch in an email. "His behavior towards female employees ... especially those he sees as opportunities is disgusting."

The company then launched an investigation into the situation. Tom Preston-Werner, the founder under question, took a leave of absence. His wife, Theresa, moved to New York to participate in a startup accelerator program, TechStars, for her not-for-profit company, Omakase.

GitHub co-founder Tom Preston-Werner is cleared of harassment allegations but still resigns.

Tom Preston-Werner, who came up with the idea for GitHub in a bar in 2007, took a leave of absence after Horvath's accusations became public. On April 21, GitHub made the results of its investigation public and said that while Preston-Werner wasn't found to have harassed anyone, he was found to have made some "mistakes and errors of judgment," according to GitHub's CEO.

In a blog post defending her husband, Preston-Werner says what some of those "questionable decisions were." Some GitHub employees felt that she had been too pushy with her own startup, Omakase, and had encouraged them to work pro bono for her in their spare time. Some employees felt that was an awkward conflict of interest.

Omakase, a charity co-founded by Theresa Preston-Werner, was recently accepted into the Techstars NYC startup accelerator program. Twitter / Theresa Preston-Werner "I am so very sorry if anyone felt that I was pressuring him or her for advice, labor, or to sign up. I truly never had that intention," Theresa Preston-Werner wrote on Medium. "I was just excited about my business and thrilled to share it with anyone who would listen ... As a result of my actions, in part, Tom left the company he founded."

For Tom's part, he is firm that he and his wife never harrassed anyone, and he's willing to get lawyers involved to protect their reputations if he needs to. He also says he's working on a new startup to do with immersive computing.

"I want to be very clear about one thing: neither my wife, Theresa, nor I have ever engaged in gender-based harassment or discrimination," Tom Preston-Werner wrote. "The results of GitHub's independent investigation unequivocally confirm this and we are prepared to fight any further false claims on this matter to the full extent of the law."

Julie Ann Horvath's Twitter explosion after news of Preston-Werner's resignation broke suggests she's still not happy. There's another engineer at GitHub she wants held accountable for "bullying" her after she says she refused to sleep with him.

After GitHub announced the resignation of Tom Preston-Werner, Julie Ann Horvath tweeted a series of complaints about how the investigation was handled and about an engineer who remains at the company, who she feels sexually bullied her.

Here are a few of the statements she made:

There may still be a lot more to this story we don't know.

There's a Medium post written by people who say they're GitHub employees that suggest a lot more to Horvath's story. It alleges that the employee Horvath says she wouldn't sleep with was actually a former friend whom she dated prior to joining GitHub. It also says Horvath spread rumors about the Preston-Werners. None of those statements has been confirmed.