After Lucifer took possession of President Jefferson Rooney, he entered a sexual relationship with Jefferson's aide and secret lover, Kelly Kline. Kelly, unaware of the possession, suggested to Lucifer that he would make a great father. Lucifer was inspired by her words and intentionally conceived a child with her.
The conception was felt throughout Heaven. Castiel also detected it and warned Sam and Dean of the potential threat this unborn child could pose. The Winchesters enlisted the help of Crowley and Rowena MacLeod to banish Lucifer back to The Cage, after which they would encourage Kelly to abort the child.
Following Lucifer's banishment from Jefferson's body, Castiel took Kelly away and tried to talk her into aborting her child. Despite being made aware who the child's real father was, Kelly allowed her maternal instincts to protect the child and she escaped from Castiel by climbing out the window of the diner they were at.
This began the hunt for Kelly Kline.
Castiel begins a long search for Kelly, and initially tries to track her down alone. Meanwhile, the angels in Heaven have come to an agreement that they should focus on terminating the unborn Nephilim. The angels begin this operation under Joshua, who leads his fellow siblings in a bid to capture Kelly.
About a month's time, Kelly is located by two angels at a diner, who proceed to corner her in a dark alley. Their attempts to kill her on the spot using Angel Blades are foiled when Prince of Hell Dagon appears and kills them both. Dagon then offers to protect Kelly by convincing her of her son's potential as a world savior. Kelly reluctantly agrees.
Lucifer, who has been imprisoned in Crowley's lair since his banishment, keeps an eye on his son from his cell, and is pleased to know that Dagon is now acting as the child's protector. Lucifer communicates to Dagon at some point with a promise to make her his Queen if things go well. From then on, Lucifer maintains telepathic communication with Dagon.
During a hunt, Eileen Leahy discovers that a Warehouse was burned down by a man who had been reported as missing for two years. She learns that the man is under demonic possession and tracks the demon (who goes by his vessel's name Dermott Culp) to a clinic. She learns from Dermott that he is a servant of Dagon and has been assigned to cover Dagon's tracks so no one would know where to find Dagon and her new ward, Kelly. Eileen relays this information to Sam and Dean.
In the absence of Castiel, Sam and Dean gain assistance from British Men of Letters operatives, Mick Davies and Renny Rawlings, who wish to partake in the mission themselves. Mick gives Sam The Colt to use against Dagon. Having learned that Kelly recently visited a doctor at the clinic, Sam calls Kelly pretending to be someone from that clinic and urges her to return and see the doctor. Kelly does, and is promptly captured by Dean Winchester. Dean delivers Kelly to the group's location. The five debate on what to do with Kelly. Sam, Dean and Eileen wish to take Kelly back to the Men of Letters bunker, while Mick and Renny do not believe sparing the child is a safe choice.
Upon discovering Kelly's absence, Dagon arrives at the group's location to retrieve Kelly. Dagon attacks the group by flinging them aside. Eileen tries to kill Dagon using The Colt, but the Prince disappears before the bullet hits her, leading Renny to get shot instead. Mick attempts to avenge the fallen operative by killing Eileen as per British Men of Letters protocol, but he is convinced not to. Because of her recklessness, Dagon now uses chains to bind Kelly to their hideout, much to Kelly's distress.
Kelvin is sent by Heaven to recruit Castiel in recapturing Kelly. Castiel agrees so that he may spare Sam and Dean the need to spill innocent blood. Castiel thus joins Kelvin and Hozai in a mission to infiltrate Dagon's hideout. While Kelvin and Hozai try to fight Dagon, Castiel heads to the basement intent on killing Kelly, but he decides to run away with her instead. Dagon kills Hozai and captures Kelvin, but becomes distressed when she finds Kelly absent. She reports back to Lucifer, who he is furious at her and promises her a great deal of suffering if she fails him again. Dagon opts to torture information out of Kelvin, before killing them.
Castiel takes Kelly to a motel as they debate over whether the child will grow to become good or evil. As Castiel had stolen The Colt from Dean as part of his mission, Dean and Sam track down Castiel to the motel to retrieve the weapon. Sam and Dean insist on making a decision for Kelly's future themselves, but before they could take Kelly anywhere, Kelly drives off with The Impala and Castiel towards the Heavenly Portal, which the angels had intended for her to pass through as a means to kill her and her child. Kelly's motives for going there are visions from her child promising a good outcome.
At the Portal, Joshua greets them but he is soon killed by Dagon, who had been waiting for them to arrive. Dagon gets into a fight with Castiel and nearly has the upperhand, until Kelly's child chooses to empower Castiel and give him the strength to incinerate the demon. Sam and Dean arrive in time to witness the Prince's demise. Castiel however, appears to have been manipulated by the Nephilim into becoming its new protector. Castiel abandons Dean and Sam at the Portal and drives off with Kelly, as a result of a vision from the Nephilim promising paradise.
At this point, the angels cease any more attempts to track down the Nephilim and Kelly. Lucifer, on the other hand, manages to escape captivity after nearly a full five months of imprisonment. He is assisted by Drexel, who helped to weaken the bindings holding Lucifer to Crowley.
Sam and Dean continue to search for Kelly with some assistance from Jody Mills. When Sam leads a team of American hunters in a confrontation against the British Men of Letters, he is informed by the Elder, Doctor Hess, of Lucifer's escape. Jody, a member of the team, kills Doctor Hess. Sam takes this new information back to the Bunker and relays it to Dean and their mother Mary Winchester. The three agree to stop Lucifer from getting his hands on his son. Crowley too joins their side as he is aware that Lucifer's freedom is his fault.
The battle leads the Winchesters to a cabin by the lake, a place intended to be the home for the newborn Nephilim. Kelly is prepared to die during childbirth and leaves behind a video for her unborn son, whom she has named "Jack". As Kelly enters labor, Jack's presence opens up a portal to an alternate reality. Sam and Dean ultimately use this portal to trap Lucifer, but at the cost of Crowley's life.
Before the portal can close on him, Lucifer escapes and kills Castiel. He then fights Mary, and both fall into the portal as the portal finally closes. Sam returns to the cabin to find Kelly dead on her bed and Jack hunched in the corner of his nursery, in the form of a fully grown adult.
The hunt renders both Heaven and Hell without a ruler, as Joshua and Crowley were killed during the event. Mary Winchester is trapped with Lucifer in an alternate reality with no known means of escape. Dean is left to watch over the corpse of Castiel, while Sam meets with Jack for the first time.
Kelly Kline, as a natural result of birthing a Nephilim, dies.
- Castiel dies again for the fifth time. This is his second death at the hands of Lucifer.
- Crowley dies for the first time since his death as a human.
- Castiel worked alongside Heaven for the first time since the conflict with Metatron. His alliance with the angels however, is solely for the benefit of Sam and Dean.