Beyond the Black Rainbow
Short Version: 
Dr. Arboria makes an institute to help people find happiness.  As it turns out, we find out late in the movie in a flashback when a younger looking Dr. Nyle talks to his now old partner Dr. Arboria while helping Dr. Arboria shoot up with the black enlightening goop, in 1966 Dr. A. dunked his partner Dr. Barry Nyle in black goop that opened up his "third eye" or his mind... he gets out of the goop, kills Mrs. Arboria by biting her in the neck, and turns into a hairless/weird eyed freak which is covers with a wig and contacts most of the time.  Resultingly, Dr. A. decides to dunk his baby into the enlightening goop.

Then the rest of the movie -- taking place in 1983 -- is Dr. Nyle having therapy sessions with Elena -- and we find out that he's getting crazier and more obsessed with her (her caretaker finds his file of "notes" which starts off like a patient file but is also filled with creepy drawings of Elena naked/in chains/anatomical drawings) over time -- setting her up to "escape" (giving her a picture of her mom, injecting her with a tracker, prompting her to kill the orderly/nurse who takes care of her) -- which she does.  Elena gets free, after crawling through the building and encountering some "experiments" along the way, and walks through some fields eventually finding a spot to sleep in the grass.

Dr. Nyle kills his wife, takes of his wig, contacts, gets out a shiny knife and puts on a motorcycle suit and pursues Elena.  He kills two random guys doing drugs and listening to music in a field  (Notably, one of the guys is Vincent from the TV show Eureka - he's stabbed in the mouth).

Then Dr. Nyle finds Elena, wakes her up and yells at her to come with him.  Then he falls over (his foot gets caught in some roots/branches on the ground) and bonks his head on a rock.  He's apparently dead with his eyes open.  Elena leaves him there and walks over towards a suburban neighborhood.

Super-Long Version:
It starts with a year title in red "1983"

Next we see hands start up a promotional video for the Arboria Institute.  Dr. Mercurio Arboria talks about wanting to help people achieve "contentment, happiness, inner peace."  He also says they use "benign pharmacology, sensory therapy, and energy sculpting."

He talks about the facility and the gardens and there are titles mixed in that say, all told, "A STATE OF MIND / A WAY OF BEING / A PRACTICAL APPLICATION / OF AN ABSTRACT IDEAL / BORN OF A DREAM / TO CREATE A REALITY / A DIFFERENT WAY TO THINK / A NEW WAY TO LIVE / A PERFECT WAY TO BELIEVE"

At the end of the video, you see him holding a glowing pyramid that glows out and there's a title for the institute.

The credits start then, we see an eyeball with the pupil dilating.  Then we see Elena.  Over the course of the film we see several sessions between Elena and Dr. Barry Nyle -- Mercurio Arboria's partner (he's mentioned in the video).  In most of the sessions that are shown, Dr. Nyle is pretty much harassing her and trying to provoke what he writes on his clipboard as, "an emotional response."  Most of his questions are pretty basic, but he has a creepy demeanor when he interacts with her.

After the first session, we see Dr. Nyle at home with, what I presume is his wife, Rosemary.  He finds her sleeping and, as they talk, she claims she was meditating not sleeping.  She says there's food for him if he's hungry.  He says he's not, she goes back to bed, and he goes into the bathroom, takes a bunch of pills, there's a weird distortion and he smiles creepily.

We then see Elena in her room.  She goes to a monitor that says, "Arboria," on it.  She puts her hand on it and flips through channels.  She settles on a cartoon.

In the next session, Dr. Nyle talks about Elena's mom, telling her that she was very desirable.  He tells her he'll give her a picture of her mother. He tells her she's looking more and more like her mother.  He's also creepily personal about the mother.

Then we see Elena looking at the picture in her room.  Dr. N. watches her on a monitor.  She goes over to a glass paneled wall, we can hear a heartbeat, the room kind of flickers and we see a flash of the pyramid.

In the next session, Dr. N. tells her he can guide her to her inner self.  She makes a weird face, eyes rolling back, and we hear her say, "I want to see my father," in voice over.  Dr. N. tells her the world is dangerous and that she'll see him again one day.

In the hallway Elena made the orderly's nose bleed.  We see her leaving after the session, in her coat with a briefcase.  She finds a drawer (the button is buzzing/not working properly) and opens it.  It contains a notebook -- the first few pages seem like a normal patient file but the drawings and things get progressively more disturbing (weird drawings of vaginas and Elena in bondage and other anatomical pictures) and she drops it back into the drawer, recoiling.

In Dr. N.'s office he answers the phone, talks to a weird electric-noise voice and then, he finds that the phone isn't plugged in.

He finds a tissue near his creepy book.  He puts it in a trash chute and then sucks his fingers.  He makes a creepy face and the background goes all melty.  He then enlists Margo, the orderly, to get the contraband from Elena -- telling her he doesn't know where she got it.

Margo talks to Elena when she brings her her dinner.  Convinces her to show her the picture and then takes it.  This upsets Elena who then does the weird eyes rolling back thing.  Margo and Elena's faces distort, then Margo is covered in blood, and she collapses.  Elena reaches for the crumpled picture out of the blood and then goes toward the doorway.

Dr. N is watching the exchange and then turns a knob up.  The pyramid we've seen periodically glows and Elena collapses in the hallway.

We see a computer screen that says, "Run Program > Sensionauts" and then we see a figure in a weird red suit walk over to Elena and inject a red tracker into Elena's neck.

Next we see Dr. N. visiting Dr. Arboria.  Dr. A. is old and grayish looking.  He talks about nurturing the heart.  He asks Dr. N to assist him and Dr. N agrees to.  He tells Dr. N that the videos make him think of a simpler time.

Then we flash back to 1966.  The picture goes to extreme black and white.  There's Dr. A, Dr. N, and Elena's mother.

The three talk about a "great journey," he's going to go on.  Dr. Nyle has an eye drawn on his forehead and the woman puts an eyedropper full of something on his tongue.  Then Dr. N gets into a pool of weird black liquid.  He sinks down below the surface.  After he’s below the surface we see a bald head with all kinds of weird stuff happening to it -- it glows red and had clouds around it, at one point his face is melting and dripping upwards, and lots of weirdness.  

Then we go to the black and white again.  There's a black dot on a white background and, after a long pause, Dr. N. comes up out of it gasping and crawls out of it.  He throws up some of the goop and then attacks the woman -- Elena’s mother -- biting her neck and killing her.

Next we see Dr. Arboria holding baby Elena with a mostly bandaged Dr. Nyle (one eye is exposed and his mouth) and Dr. A. says, “Your mother’s reabsorption into the cycle of life won’t be for nothing, my darling Elena.  You will be the dawning of a new area of the human race and the human soul.  Let the new age of enlightenment begin,” and then he dips her into the goo pool.

We come back to old Dr. Arboria and Dr. N. Helps him shoot up some of the black goo.  We see his arms and veins all over are black with it, but he insists Dr. N. shoot it in between his toes because he “doesn’t like to see.”  He asks Dr. N. about Elena, Dr. N tells him she’s doing well, then shoots the drug into him and Dr. A. Reacts as if he’s instantly high saying, “Wonderful, isn’t it beautiful?”

When he’s shot up, Elena gasps and we see her face and his fade in and out and then their eyes overlap and then the shot fades to Dr. Nyle’s in red light.

Dr. Nyle goes home and finds his wife sleeping with the TV on.  President Reagan is talking about something.  He goes to the bathroom and takes of his appliances -- pulls of his wig and painfully takes off his contacts and then he puts on a motorcycle looking suit and he also gets a knife from a draw or box.  

He goes in to talk with Rosemary and she’s surprised to see him without his appliances.  They have kind of an argument.  She asks if he’s okay and he basically tells her he’s more evolved now and “can see what other’s cannot see,” and that he was chosen, mentioning going through the eye of God and something funky about the beauty of a black rainbow.  He grabs her and tells her she’s nothing, “less than nothing - just spit in the wind,” and proceeds to poke out her eyes and crush her skull in his hands below the level we can see.

Following that, we see Elena busting out of the institute.  It takes a long time but, essentially, she takes the elevator and crawls through some ducts.  She see the figure in the weird red suit from earlier -- it takes it’s mask off and it’s a creepy looking/weird eyeballed thing.  She also encounters a scary dude in a full body straight jacket who’s all white faced and bulging eyeballs who tries to eat her -- she gets out of the room and closes a glass panel and he’s all tongue/biting at the glass trying to get her.  Eventually, she makes it through the gardens and outside.  She looks at some pretty things - the stars and a bug - after walking for awhile and then she lays down in the grass and goes to sleep.

Meanwhile, Dr. Nyle goes back to the institute looking scary (his eyes are black and green with little white part and he’s bald/hairless).  He calls out of Elena but can’t find her.  He sniffs her bed and moans and then we see him looking for her with the tracker in the car.  He stops at a fallen tree, gets out, and finds two dudes doing drugs together around a campfire.  One of the two is off peeing alone and Dr. Nyle stabs him through up through the face from below.  Then he goes over to the other guy (the guy who played Vincent on Eureka) and asks if he knows where Elena is and if he f**ked her.  He answers no and is crying/scared, then Dr. Nyle stabs him through his mouth.

Elena gets up from where she’s been sleeping.  Dr. Nyle says, “You look so beautiful when you sleep.  Sweet.  Sweet Elena.  I found you.  It’s okay.  Come to me, okay.  Lena, c’mon, c’mere.  Come to me, Elena.  Elena.  Come to me.  Come to me.”

She won’t come to him.

Then he yells, “Come to me!” and tries to advance on her, but his foot gets caught in some roots or something, and he falls over hitting his head on a rock.  He’s seemingly dead with his eyes open.

Elena continues walking and she comes upon a road and a typical tract housing development and then the credits roll.

**At the very end of the credits there’s a brief display of one of what looks like a doll in a red suit like the figure that put the tracker in Elena’s neck but I have no idea if that was significant at all.

Thanks Linsey!