Several songs on the movie soundtrack sound sinister. "1966: Let The New Age Of Enlightenment Begin" consists largely of an ominous Drone of Dread.
The sheer amount of control that Barry has over Elena is chilling. He keeps her prisoner in the Arboria Institute's lower levels, monitors her through video cameras, denies her any mental stimulation aside from a small TV set in her cell, suppressed her power through a pyramid device that renders her catatonic, plays sick games meant to manipulate her emotions, and clearly has a sexual interest in her.
Barry doesn't actually lose his shit until the third act, but from the beginning it's clear that he's basically a bomb waiting to go off.
There's also the implication that the reason the facility is so empty is that he killed most of the staff long ago.
The photo of Elena's mother is black-and-white, inky, and ghostly. She looks less like a person and more like an apparition.
Margot finding Barry's notes about Elena, which are filled with some rather... explicit drawings that raise some troubling questions about the nature of his obsession with her. The fact that he has explicit drawings of a minor whom he is keeping captive make the notebook drawings worse.
One of the notebook drawings depicts a human with black tendrils coming off of their head, connecting to several other humans who have black tendrils coming off of their heads. The drawing might represent a hierarchy of mind control, suggesting that Barry wants to use Elena to mind control others on his behalf.
The flashback to Barry's trip. The whole thing is visually an homage to Begotten, which should be enough to qualify as Nightmare Fuel in and of itself, but the actual trip is downright horrifying. It's essentially a series of hellish images, including (1) Barry made out of weathered, porous stone, with a strange light glowing within him, (2) billowing, garishly colored clouds and water, (3) Barry's head liquifying in a lurid black and pink hellscape, (4) otherworldly smoke pouring into Barry's skull, and (5) Barry as a man made out of glowing red amber or glowing hot metal, as if he is being reforged into a new being.
After he reemerges from the mysterious vat that showed him the images, he vomits up copious amounts of the black liquid and whimpers in fear and pain. He then proceeds to bite into Anna (Elena's mother) like her throat is an apple. He does this while coated from head to toe in a strange black liquid, which makes things even creepier.
Bonus footage on the DVD shows a wax humanoid head that slowly melts from exposure to a stream of hot air from above. The filmmakers may have intended to include this and other disturbing images in Barry's psychedelic experience!
After Barry's 1966 psychotic break and Anna's murder, Dr. Arboria decided that it would be a great idea to submerge his infant daughter in the same black liquid that corrupted Barry. Viewers are mercifully spared the actual image of Arboria doing so, but the thought of him submerging her in the ooze, and of baby Elena entering the same otherworldly hellscape that Barry did, is horrifying.
Barry killing his wife by crushing her eyes with his thumbs.
Elena crushing Margot's head using her telekinetic powers.
Elena coming across a mutated man in a blood-stained straightjacket. The man looks and acts like a ravenous zombie, and was probably one of the Arboria Institute's experiments gone horribly wrong.
The Sentionaut has a tall, humanoid body and the face of an infant. Like the creature in the straightjacket, he was probably the result of Arboria Institute experimentation gone wrong.
