In Netflix's new horror film Eli, a boy with an autoimmune disorder (Charlie Shotwell) is taken to a remote treatment center in a last-ditch hope to cure his condition - but the ending reveals that there's more to his illness than meets the eye. Directed by Ciarán Foy, Eli stars Lili Taylor as the enigmatic Dr. Horn, Max Martini and Kelly Reilly as Eli's parents, Paul and Rose, and Stranger Things' Sadie Sink as a local girl called Haley, who befriends Eli through the glass of the conservatory.
Eli is told that he has to undergo a series of three treatments to correct his gene mutation, but the first two seem to make him even sicker than before. To make matters worse, he's plagued by the ghosts of previous patients, who suggest that he's being lied to and at one point try to drag him outside. Eli realizes that the word "LIE" the ghosts are spelling out actually says "317" when viewed upside-down, and with a little prompting from Haley deduces that it must be the code to the medical wing. He goes there, and finds medical records showing that all three previous patients died after receiving the third treatment.
Despite Eli's protests, he is dragged to the medical wing. He manages to escape and flees to Dr. Horn's room, where he discovers a secret passage leading down to a strange chamber. Inside is an altar and a pit covered by a stone with a religious symbol on it. Before he can make sense of what's happening, he's locked inside the chamber by Dr. Horn. Exposed to non-purified air, Eli starts to hyperventilate, his skin turning red, until eventually he collapses. He doesn't die, however - because he doesn't really have an autoimmune disease at all.
Eli Isn't Sick - He's the Son of the Devil
Eli's ending twist is that Dr. Horn isn't just a doctor, but a nun, and she's been trying to use gene editing to rid the Devil's children of their corruption. Unfortunately she hasn't had much luck so far, as Rose learns when she discovers the bodies of the three previous patients in the ritual chamber's pit, their bodies wrapped and covered with symbols to prevent their evil escaping (unsuccessfully, as it turns out). A tearful Rose later reveals to Eli that when she was having trouble getting pregnant, her prayers were ignored by God, so she started praying to the Devil instead. He offered to give her a son, promising that Eli wouldn't be like him - which was, of course, a lie. This explains why Paul acted colder towards Eli: he knows that he's not his real son, but the result of an unholy affair with the Devil.
The "treatments" that Dr. Horn has been carrying out are a mix of medicine and exorcism. Eli's IV drip was actually holy water, and the injections he was given were tannis root, designed to suppress his true nature while Dr. Horn worked on his genes. When it's clear that the treatment has failed once again, Dr. Horn offers to at least save Eli's soul by performing a rite and killing him with a holy dagger. Paul restrains a distraught Rose after she tries to release Eli, and the ritual is performed, but Eli uses his telekinetic powers to stop the dagger from piercing his chest. He then puppeteers the bodies of Dr. Horn and her nurses, turning them upside down with their arms spread to form an inverted cross, before setting them on fire.
Paul tries to stab Eli with the dagger to complete the ritual, but Eli stops him and uses his powers to crush Paul's skull. With red skin and demonic eyes, he sets the house on fire and leaves - sparing only Rose, who tried to help him and begs for forgiveness for everything she's done to him. But Rose isn't Eli's only ally in the world.
Haley is Eli's Half-Sister, and Has Been Guiding Him
Through Eli, it's suggested many times that there's more to Haley than just a bored local girl. She knows exactly where Eli's room is, throwing rocks at the window to get his attention, and when he first goes to meet her at the conservatory she shows him a "magic trick" where she sets a twig on fire in her hand without being burned by the flames. She also says that Dr. Horn doesn't like her and won't let her in the building. It's Haley that assures Eli other patients have seen ghosts as well, and she first suggests that the number "317" might be a code for a door. When Eli tries to escape before his final treatment, Haley encourages him, telling him, "You're so much stronger than the others."
After Eli escapes, Haley is outside waiting for him. She explains that she's also one of the Devil's children, and that the three previous patients were their half-siblings. She couldn't actually tell Eli the truth or break him out of the house, because their father insists on his children earning their place, but she could guide him in the right direction. After he frees himself, she offers to take him to their father - and instructs Rose, who has now accepted Eli's true nature, to drive the car.
Why Eli Got Sick When He Went Outside
One detail that isn't explicitly explained in Eli's ending is why exactly he appeared to have a strong allergic reaction when exposed to normal air, even by a simple tear in his Hazmat suit. Dr. Horn tells him that his sickness doesn't come from without, but from within, and she also reveals that she's been working with his parents for a long time. Putting all this together, it's possible to conclude that there was an extra element to Eli's bubble room at home, his Hazmat suit, and even to the airlock in Dr. Horn's house: they weren't simply keeping the air purified from germs or dust, but were religiously reinforced to keep Eli in purified "holy air" that prevented his true self from emerging.
After killing everyone except his mother and setting fire to the house, Eli steps outside and his red skin and demonic eyes fade away, indicating that the allergic reactions he's been having were simply the first stage of a transition that his parents had previously managed to prevent being completed. With the full knowledge and understanding of what he is, he's able to be like Haley: appearing normal to hide his demonic side. As for what he will do once free... well, it's probably nothing good.