(CNN)In the spring of 2015, LeeAnne Walters had been getting the runaround from local officials about the brown water that was flowing from the taps in Flint.

Her twin boys were getting rashes. One was showing signs of stunted growth. "We had to figure out what was going on," she said.

So she turned to the Environmental Protection Agency, the federal government agency that regulates drinking water. Walters was confident the agency would come in, find answers and fix things -- quickly.

That's not what happened. This story doesn't end in spring 2015.

"Absolutely not," Walters said.

Instead, when EPA Region 5 Director Susan Hedman found out about the astronomically high levels of lead in Flint water, emails show she tried to keep it under wraps.

Hedman resigned in January amid the crisis. It has become clear the EPA did not live up to its mission in Flint.

The water there had become tainted with lead and other toxins. It had been a breeding ground for dangerous bacteria such as Legionella and E. coli.

But for several months, Hedman did little to fix the problems.When Walters made the call to the EPA, she was connected to scientist Miguel Del Toral, the only person in government who Walters considers a hero in this story.

Del Toral had been assured by the state of Michigan that Flint's water had "optimal" corrosion control. But Walters, who had taken to spending nights and weekends researching water chemistry on her computer at home, checked the city utility operational reports and found that orthophosphate, the chemical used across the country for corrosion control, wasn't on the list of chemicals being added to Flint's water.

Without corrosion control, water eats away at the pipes that carry it to people's homes. In places such as Flint, with aging infrastructure, many times that means lead pipes begin leaching lead into the water.

Lead is a deadly toxin that affects the brain and nervous system. Its damage is irreversible, and it can have a profound and lasting effect on children.Walters knew her water was tainted with lead. The levels were so high that they were twice the level considered to be toxic waste.

The EPA says anything over 15 ppb is unsafe, and Walters' home tested at more than 13,000 ppb.

"I don't think there's words for that. It was one of those grab the counter top, oh my god, kind of moments," she said.In June, Del Toral wrote a memo highlighting preliminary findings of "serious concerns for residents" and "violations" of federal regulations. He also wrote that the city of Flint was using a flawed method of testing water for lead and still finding "lead levels in excess of the lead action level."

But despite the strong language and warning from one of the agency's top scientists, Hedman and the EPA did not immediately act.

Instead, Walters said Del Toral was silenced, told not to talk about Flint and not to talk to people in Flint.

Emails show Hedman downplayed the memo, writing that Del Toral "inappropriately released a draft report." In another email, she offered experts to the city, but the city had no control over the crisis, which was being handled by the state of Michigan.

Emails show that it was 11 months from the time that an EPA official first expressed concern over high levels of lead in Walters' home -- and seven months from when Del Toral wrote his draft memo -- until the EPA issued an emergency order in Flint.EPA management declined several requests for an on-camera interview. It initially said in a statement that it did not release Del Toral's memo publicly because it contained personal information but says it was circulated among top staff in Region 5 who were "working to require Flint to implement corrosion control treatment."

After CNN aired a television piece on Del Toral's memo, the EPA said Del Toral was and still is a "valued" employee, and it said in response to the fact that the EPA did not impose an emergency order for nine months, agency officials sent CNN a detailed timeline and said "EPA repeatedly tried to get the state to take action ..."

An earlier statement from the EPA said the ability of the EPA to oversee was "impacted by failures and resistance at the state and local levels."

After the memo became public, Jennifer Crooks, the EPA's Michigan program director, told the Michigan Department of Environmental Quality that it could tell journalists and lawmakers that it never received the memo, even though other emails show the EPA was keeping state officials abreast of Del Toral's work, writing, "If the Legislature or whoever might say you all were cc'd, you can truthfully respond ... you all never received the report from Miguel."

An EPA spokeswoman said Crooks' email was supposed to convey that the EPA would handle reporters' calls about Del Toral's draft memo because the Michigan Department of Environmental Quality (MDEQ) had not actually received a copy from the EPA.Marc Edwards, the world-leading Virginia Tech researcher who blew open the Flint crisis and obtained thousands of documents through records requests, says he was appalled at how the EPA and MDEQ handled the draft memo leak.

Edwards later tested the water at Walters' home and at almost 300 other Flint homes, with horrifying results. In August, he released his findings, but the state didn't believe them until October, when the state relented and switched the water supply back to the Great Lakes.

A Congressional Research Service report released February 16 said that the EPA must use its power to bring a water system into compliance with the Safe Water Drinking Act 30 days after finding a problem, and that "EPA has not used this authority in Flint."

It also found "concerns that EPA did not quickly intervene and notify the public."

But after a number of media outlets quoted these lines, the report was rewritten and updated on March 2. Several things were deleted, or changed, including those two lines.

The report now says that "Events in Flint have raised questions regarding the ... scope of EPA enforcement and notification authorities under (the Safe Water Drinking Act.)

A spokesman for the Congressional Research Service said this report and its analysis was done "exclusively for Congress. Our reports are written specifically with our congressional audience in mind, and updated as necessary to reflect evolving conditions."Two current EPA employees have been watching all of this unfold with little surprise. Ron Harris and Carolyn Bohlen are both EPA employees and have been for decades.

"I thought, 'Well, here we go again,' " Bohlen said.

In July, they testified before Congress, saying Hedman retaliated against them after they investigated a sexual harassment claim in the EPA Great Lakes region office and reported that EPA management in Region 5 had known about the misconduct for years.

Bohlen, then the director of the Office of Civil Rights, had just received a federal employee of the year award. She had been hand-picked by Hedman to run the department. But when Bohlen and Harris presented the findings of their investigation, Hedman's senior administrator, "threatened us, intimidated us, he beat on desks, he stuck his finger in my face, screamed, hollered, he described our work as bullshit," Harris said.

"I had never in my life seen anything of that nature. I was appalled," Bohlen said. "... We did our jobs. We did what our jobs required us to do. So, perhaps we did it too well."

Harris and Bohlen said they were soon notified they'd been reassigned. Both filed complaints with the Equal Employment Opportunity Commission and settled their cases.

What happened in Flint seemed like an all-too-familiar scenario to Bohlen and Harris.

"You have someone who is a very dedicated employee, very serious about his work," Bohlen said. "Miguel Del Toral. Very effective employee, who presented the information very well and it was disregarded."

Congress is holding another round of hearings, this time over what happened in Flint. Hedman is expected to testify.

In addition, the EPA's Office of Inspector General also has two open investigations into Region 5 of the EPA: one on how the Flint water crisis was handled and one on overall accountability. A source told CNN there is a "culture issue" of protecting the department and dismissing those who speak against it or raise problems.

"We're embarrassed," said John O'Grady, the EPA union president in Region 5. He said Hedman was a micromanager and many of her employees felt bullied by her.

"I think there's a problem that we're not transparent enough," he said. "They don't want to act on problems. Maybe they're worried about the political implications of problems."

Dismissing employees who are trying to raise concerns, Edwards said, undermines the EPA's mission.

"They are not worthy of the public trust," he said. "They are unscientific. They care more about their reputation and perceptions than they do about endangering little children."