Maybe someone here can help calm my nerves and let me know if it’s over for me with this agency. 

I had my 1st polygraph recently and I thought it went rather well. The lady was very nice but she told me I hadn't passed the life style portion, specifically 3 questions: Serious Crime, Drug use in 2 years and falsifying information on my security forms. I was rescheduled for the next day to do that part over again. 
The next day, I met the new polygrapher and on the way to the room she came off incredibly nice, we made small talk and she even made a few jokes, but as soon as the door closed she was a completely different person. She grilled/interrogated me for nearly 5 hours on those 3 questions. Needless to say I haven't committed a serious crime and haven't done any drugs in 13 years nor did I lie on my forms. She didn't believe me and kept telling me I wasn't being honest and that unless I didn't confessed she would have to end the poly.
I told her I want this job more than anything and I'm being 100% honest I haven't done anything wrong. She said "well unless you don't have anything to confess I have to end this." She unhooked me from the machine and told me I failed and that she would be surprised if I got a call back to do a retake. She told me there was no way I hadn’t done drugs in college, I’m allergic to marijuana, one puff and my throat constricts to where I can’t breathe. She said I could have done coke then, etc. 
In total, she ran at minimum of 10 charts but could have been up to 15 saying she needed more data. Every time she came back to the room she said "your holding back, you’re not giving me everything."  She did tell me that I was passing one chart but then would fail the next which must have been because “I’m lying.” I wasn't doing anything different the entire time. Half the poly was verbal "Yes" or "No" the other half was nodding and shaking my head. I was so upset that she told me I failed and that it was pretty much over for me with this job I honestly almost cried. She saw how upset I was, she told me in a soft voice, “I’ll work with you and go to bat for you if you just confess to what you have done.” I told her I haven't done anything wrong and I don't know what you want me to say. At that point she told me again that I failed, she opened the door and escorted me back to the lobby. 
Very strangely, as soon as we were out of that room she was incredibly friendly to me. I was nearly in tears from my 5 hour interrogation and hearing I wasn't getting this job and she’s laughing and carrying on making small talk with me.
I honestly don’t know how I could have failed. I live a simplistic life, don’t drink or do drugs, I go to church, never been in trouble, graduated Valedictorian and had amazing references including the Mayor and now because of this polygraph I think my chances are over.
What do you think? Did I truly fail or was this just some trick to see if I would crack? The background investigator did ask one of my references “what it would take to make me crack.” Thought that was weird. 
O and one more thing, near to the end she said because I was such a liar she feared I was a threat to national security and I must be trying to infiltrate their agency for malicious reasons. Absolute craziness. 
What do you all think?

Your encounter with the polygraph process is not unique. Five hours on three questions is absurd. This is their modus operandi and unfortunately, people like you and I can easily fall victim to the fraud and abuse.

It’s all too common in this situation for overly self-conscious people to “fail” under duress. Maybe she saw something, but more likely it was nothing and she was just pulling your chain. Emotions such as fear, anger, panic, anguish, humiliation, shock, worry, frustration, resentment, disgust, embarrassment, shame, annoyance, anticipation, distrust – all produce physiologic reactions – which are unique for each individual. They illegitimately classify any physiologic reaction you have as “deception”.  To be clear, there is no specific physiologic reaction that can be accurately identified and classified as a “lie”, and any attempts to do so is deceitful.

This part is very important – for some people, once the polygrapher tells you that you didn’t “pass” on a certain question, it’s almost impossible to not, not react again when they ask you the question again (and again and again and again).  You’ll never be able to get back to the place you were before they questioned your honesty. The butterflies will get to you.  I’ve explained it many times like when you’re driving down the road and flashing lights suddenly appear in your rear view mirror.  You know you haven’t done anything wrong, but you still get the butterflies.  It’s an uncontrollable physiologic reaction.  It’s not what you’re thinking about the question that causes your reaction, it’s what you’re thinking about your reactions will be to the question, that cause your reactions.

30 years ago, Congress passed the Employee Polygraph Protection Act because the theory behind the polygraph is based on faulty logic and assumptions.  Incredibly, the government was granted an exemption to the Law, and is permitted to continue administering the polygraph.  The worst part is that they know it’s not accurate. They’ve even stated that it’s okay to “crack a few eggs to make an omelet.”  It’s proven to be biased against honest, self-conscious people like you and I, and the truly bad people can easily pass it, simply by controlling their emotions. (See Ed Snowden, Aldrich Ames, etc.)

I’m sorry you had to suffer though this highly abusive process, just know that you are not alone. From what you said that she told you, I expect she chalked you up as another potential insider threat – thus proving her worth and keeping her job. Probably helped her to meet quota too.

In the end, you’re better off not working for that agency anyway. They now conduct periodic polygraph screenings of existing employees – you would have had to risk losing your career, your reputation and your sanity, every five years.