In Providence, Rhode Island, a prostitute named Gloria Sytnik sits in an apartment room filled with angel souvenirs. She switches the television to a televangelist but quickly turns it off. The lights flicker and the TV comes back on, and the televangelist insists that the Lord is talking to his audience. The prostitute is unable to turn off the television, and the room begins to vibrate. A glowing white light streams through the door and a figure appears within the glow.
Sam poses as an orderly and comes to see Gloria, who is locked up in a criminal sanitarium. She insists that what she saw is real, but doesn't appear disturbed or unbalanced. He asks what she saw and Gloria explains that she stabbed a man in the heart because it was God's will. She tells Sam that an angel came to her in a glow of light, filled her with peace and assurance, and told her to smite an evil man who was guilty to his deepest foundations. The angel told her to wait for a sign, and she saw it next to a doorway the next day.
Dean is at the motel enjoying the massaging bed when Sam arrives, and complains that he's locked down because he was on the television as a bank robber after the events in Milwaukee. Sam admits that Gloria seems sane, but her victim, campus librarian Carl Gulley, had no dirt in his background. They figure that something is going on because it's the second murder. Dean insists that there's no such thing as angels, and he says he's never seen one. He figures it's a demon or spirit that is tricking people into committing murder, but Sam isn't so sure. He's checked Gloria's apartment and there's no trace of spirits. The brothers go to Gulley's home to check out the sign the angel supposedly left. There's a discarded angel decoration on the porch, and an open gate on the side. The brothers investigate and find a cellar door leading down into the "deepest foundations." They go down and Sam notices a fingernail embedded in the wall. They start digging and find a skeleton buried in the basement.
A drunk, Zack Smith, is sitting in his apartment when the room starts to shake. A holy light fills the room and shines in Zack's face. He smiles and steps forward. A little later, Zack is walking down the street and sees a glow coming from a house. Zack nods, goes to the door, and knocks. A man answers the door and Zack stabs him in the heart.
At the motel, Dean is monitoring the police channels when Sam returns. He's confirmed that three students disappeared at the library where Gulley worked. Dean tells him that Zack killed someone and then confessed to the police, and he got the victim's address. The Winchesters break in and Sam uncovers dozens of emails from the victim, Frank, to a 13-year-old girl. The last email set up a meeting that would have occurred later that day. Dean admits that it's unusual for a spirit to kill criminals, and then finds a flyer confirming that Frank and Gulley went to the same church.
The brothers go there and talk to Father Reynolds, presenting themselves as churchgoers. Reynolds insists that the church is needed more than ever, and admits that all of the victims were parishioners. He doesn't believe that angels told the killers to strike. Sam notices a painting of an angel, and Reynolds describes Michael, a warrior of God. As they go, Dean notices candles on the step, placed in honor of Father Thomas Gregory. Reynolds explained that Gregory was shot for his car keys on the steps two months ago, and there was no time to administer last rites. He was interred in the church crypt. Since then, Reynolds says that he's been praying for divine intervention to deal with all of the violence in the neighborhood. Dean figures that the "angel" is Gregory's vengeful spirit, but Sam suggests that God has answered Reynolds' prayers. When Dean wonders why Sam is so willing to embrace the idea of angels, Sam admits that he prays every day.
Sam and Dean go to the crypt and look around. As Dean goes on ahead, a statue of an angel starts vibrating and a glowing light beams into the room into Sam's face. When Dean returns, he finds Sam unconscious on the floor and wakes him up. They go to the church and Sam explains that he saw an angel, and it told him to seek out a man who would commit a crime. Dean doesn't believe it, and notes that their mother used to say that angels were watching over them. But she died and nothing protected her. Dean insists that there's no such thing as angels but he has proof they're dealing with a spirit. They go back to the crypt and Dean confirms that wormwood is only growing on Gregory's marker. Sam isn't convinced, and Dean proposes that they use a ritual from John's journal. If it's a ghost, they'll summon him. If it's an angel, it won't show and they'll have positive proof.
As the brothers get their ingredients at a grocery store, Sam sees another customer glow with the sign that the angel promises. He insists on following the man, but Dean stops him. Sam says that he just plans on trailing the man, but Sam tells him to perform the séance while he follows the man. The customer picks up a woman, gives her flowers, and they drive off together.
At the crypt, Sam begins the ritual. Father Reynolds comes in and demands to know what's going on. He escorts Sam to the door, but the angel appears again. Sam tells Reynolds that it's the spirit of Father Gregory, and Gregory says that he's come in response to Reynolds' prayers. The spirit asks why Sam hasn't gone on his mission, and Sam explains that he's a spirit, not an angel. Gregory insists that once he died, he learned everything, and he's there to help Reynolds.
Dean loses the couple in traffic.
Gregory insists that he's offering sinners redemption by letting them kill for the Lord. Sam points out that the killers are locked up, but Gregory insists that it's justice. Reynolds disagrees and warns that Gregory is not performing God's will.
The man from the store pulls over and tries to kiss the woman. When she refuses, he slaps her and locks her in, and then draws an x-acto knife. Dean smashes in the car window and stuns the man out before he can harm his date. Dean helps the woman while the man drives away, and Dean goes after him.
Reynolds tells Gregory that it's time to rest, and asks to give him Last Rites. Gregory says nothing and Reynolds begins the ceremony. The spirit fades out in a blaze of light.
Dean follows the man through the streets A truck brakes to a halt ahead of him and a pipe flies off, impaling the man.
Later, Dean returns to the motel and Sam admits that his brother was right. Dean takes a drink from his flask and offers it to Sam, who admits that he wanted to believe so badly in good that he accepted the possibility it was an angel. Dean says that he'll watch out for him, but Sam says that it isn't enough and he had hoped some higher power was watching over him. Dean admits that Gregory's spirit was right, and the guy in the car was bad news. He tells Sam that the man is dead, and isn't sure what to call it. When Sam asks, Dean admits that it might have been God's will.