They arrive at the stables, and Alan is angry. Jill says this is a perfect place, and asks Alan if he would rather go home to his father. She says they cannot go to her place because her mother does not like when she brings back boys. Alan keeps saying no, and says that "them" is the problem. Jill realizes that he has a problem with the horses seeing them, so she takes him into the barn adjacent to the stable and shuts the door.
Dysart is shocked that Alan would consent to doing something like this in "The Temple" or "The Holy of Holies," but Alan says there was nothing else he could do, because he could not tell her what horses really mean to him. He tells Jill to lock the door. He describes the barn to Dysart, specifically mentioning the six horses that were behind the locked door.
They begin to kiss, but every few moments Alan is distracted by the sound of hoofs in the stable. They begin to undress, and Alan lays her on the ground. Suddenly the sound of Equus fills the room, and hooves smash on wood. Dysart asks what happened next—Alan says he went through with it and "put it in her," but Dysart does not believe this and keeps insisting that Alan give him the truth. Finally, Alan admits that he couldn't see her—every time he kissed Jill, a vision of Equus got in the way. Every time he touched her he felt Equus beneath him.
Finally he stops kissing Jill, who realizes something is wrong. She thinks the problem was that he was not aroused, and says she understands, but Alan starts yelling at Jill to get out. He picks up an invisible pick and begins to brandish it in her direction, demanding she leave. Jill just wants to talk, but finally she puts her clothes on and, frightened, runs out of the barn.
Alan stands alone and naked, and he says that Equus could see everything through the door. He begs Equus to forgive him, saying that what happened was not really done by him. He promises to never do it again, and Equus in response says "Mine! You're mine! I am yours and you are mine!" and tells Alan that he will see him everywhere, forever. Dysart begins to take on the role of Equus, bellowing that Alan's God, Equus, will always see him. In response, Alan shouts that noble Equus sees nothing, and he stabs out Nugget the horse's eyes. He goes and stabs out the eyes of five more horses as well. The blind horses begin to trample around them, and he shouts at them to find him and kill him, grabbing at his own eyes.
As Alan convulses in his office, Dysart throws a blanket around him and lets him cling to him. He tries to soothe Alan, telling him that it is finally all over now and Equus will leave him alone. He promises to make Alan well and get rid of the nightmares. He tells Alan to sleep, and he does.
But after Alan has fallen asleep, Dysart says that he lied to him; Equus will not really go away that easily. He says that if and when Equus does leave, he will take parts of Alan with him. From where she has been standing farther back onstage, Hesther reminds Dysart that Alan is in pain, and tells him once more to take it away. Dysart finally acquiesces, and says he can make the boy normal and acceptable to himself, but this would more likely make him a kind of ghost.
Dysart describes what he will do to Alan: heal him of his mental and physical scars and send him into the normal world where horses are chained, tethered, or made extinct. He says that in the normal world, humans are tethered right beside these horses as they go through their monotonous lives. He says that perhaps Alan will even come to find sex funny, and feel nothing but human flesh on his. Through all of this, Alan will no longer be in pain.
But for Dysart himself, it will never stop. He admits that he will never be able to fully know exactly what he does in this office, as a psychiatrist, but whatever it is, it is terminal and irreversible. He says he needs a way of seeing in the dark, but right now there is a sharp chain in his mouth that will never come out.
As previously discussed, Jill was introduced as a test for Alan to determine whether or not he could redirect his passions to something that is more normal. In this section, he clearly fails. As he kisses her, Jill becomes Equus to him, and he cannot separate the feeling of her skin from the feeling of the horse's. He originally tells Dysart that he was able to go through with it and have sex with her, which shows that he wants to do what is expected of him. Eventually, though, it proves to be too much for him and he fails this test.
Dysart compares the barn and stables to a temple, which Alan agrees with. By having sex inside of it, Alan would be desecrating Equus' sacred temple, his place of sanctuary. This setting is extremely important; had Jill taken him back to her own house, perhaps he would have been able to go through with it, disappointing his god but rising to the expectations society has for him. But as the stable is his place of worship, Alan cannot bring himself to so blatantly defile it.
The reason it is so difficult for Alan to have sex with Jill is because it would be a clear betrayal of the intimacy he has with Equus, his god. He had only ever shown his vulnerable, naked body to a horse. He had established this unique physical connection through his midnight rides, and by sleeping with Jill he would be giving that connection up for someone else. Equus speaks to Alan after, and his words confirm the exclusive nature of their relationship: "Mine! You're Mine! I am yours and you are mine!"
When the semantics of Alan's crime were first revealed at the beginning of the play, the way was paved for a recurring motif of eyes and seeing. This motif has been particularly prominent in Act II, and at the end of the play, it naturally explodes when Alan blinds the horses. Eyes have long been called "the window to the soul." For Alan, looking into a horse's eyes provided a way to connect with his gods and understand them in a way that he otherwise could not. But he never realized the consequences of having his gods look back, not until he felt their betrayed gazes on him while he lay with Jill. Equus repeats, over and over again, that he can see Alan at all times; this proves to be too much for Alan to bear, so he destroys this omniscient connection by blinding them.
Throughout the play, one horse has captivated Alan in particular: Nugget. Nugget has been the physical manifestation of Equus for as long as Alan has known him. But that night in the stables, Alan blinds not only Nugget, but five other horses as well. This exemplifies his earlier statement that Equus lives in all horses, not only just one. Equus is in the spirits and souls of horses, and Alan had to blind as many of them as possible to prevent them from seeing his sins. But since Equus does live in all horses, Dysart is right: he will not go away that easily.
By the end of the novel, Dysart has fully adopted Alan's pain as his own, in the way that he has for so many children that came before. He wears the chain in his mouth that Alan loathes, the chain that represents confinement and a loss of freedom. His final monologue that closes the show is extremely powerful, and it wraps up the numerous themes that this play has discussed. He reiterates that society's conception of 'normal' is not as ideal as we make it out to be, and that psychiatry's erasing of 'madness' actually means the erasing of passion, which is frighteningly permanent. Through his profession he can eliminate pain, yes—but is this pain truly self-inflicted, or does it come from a convoluted society that prizes 'normal' above all else? Peter Shaffer's Equus argues the latter.