Angel goes on Tibetan retreat to mourn Buffy's death, but meets demon monks. A still-traumatised Fred is staying in her room. On Angel's return, Cordelia has a shattering vision "these visions are killing me" of a vampire attack. The team rescue two students, and Angel dusts a vampire he knew back in his Angelus days. Her vampire lover swears revenge, and has his heart removed to become invincible, for a while. Angel wonders why he is not equally as devastated by Buffy's death. Darla is pregnant.
Cordelia's visions start physically injuring her, causing serious cuts and burns. Lorne discovers these new visions aren't coming from The Powers That Be at all, but from Wolfram & Hart. Eventually she is on the brink of death. Lilah Morgan blackmails Angel into getting an evil prisoner released from a demon fortress in exchange for curing Cordelia. He does so, but then kills the creature sending the visions, and warns Lilah he will kill her next time she uses one of his friends.
Some gang is out indiscriminately killing demons, both evil and assimilated. Gunn suffers a conflict of loyalties when he discovers it's his old gang, killing for fun. It leads to a tense showdown at the Host's bar, during a still-traumatised Fred's first trip outside the hotel.
An old man has been switching bodies with fit young men and having a good time, but on switching back, the young men burn up. The team investigate, and the old man switches places with Angel. He realises that now he is a vampire, he won't burn up the body, and can stay young forever. It takes the team a while to discover what happened (leading to some amusing misunderstandings, with Wesley and with Lilah), but get Angel back.
Fred's parents track her down to the hotel, but she flees from them in panic. They finally find her in a bus station, and she explains that if they see her like she is, she will have to admit the last five years really did happen. A giant bug attacks, and Fred's mother splatters it with a bus. Fred agrees to go home where it's safe, but on the way to the airport, she realises more bugs will attack the hotel. She returns to the hotel and saves the gang from a multiple giant bug attack, and decides to stay.
Billy, who Angel rescued from the hell dimension to save Cordelia [ 3.2 That Vision Thing ], is on the loose. His touch makes men violent against women -- Lilah is one of the first to suffer. Cordelia feels responsible for Billy's presence, and goes to hunt him down. Wesley gets infected, and starts hunting down Fred. She smashes him with a fire extinguisher. Cordelia catches up with Billy, and is about to kill him when Angel intervenes. They fight, and Cordelia is again about to kill Billy, when Lilah shoots him. Wesley is devastated by what he did, and nearly did, to Fred.
In a flashback, we see Holtz torturing Angelus, who has killed all his family. Darla confronts Angel with her pregnancy. It is driving her mad because the child has a soul. Darla bites Cordelia, which gives her a strange vision. Angel finds himself unable to kill Darla, because of his child. A prophecy points to the rising, or birth, of a creature that will destroy, or purify, all the earth. Everyone thinks it is about the child. Then in a secret ceremony the demon Sahjhan reanimates Holtz.
Wolfram & Hart learn Darla is back, because they have bugged the hotel, and set out to capture her, but run afoul of Vampire hunter Holtz. Darla goes into labour.
Holtz learns Angel has a soul, but continues to hunt him. Darla admits she loves the baby, and is terrified what will happen when it is born and she goes back to being her old self. But she is having trouble with the delivery, and they all fear it is dying inside her. To let it be born safely, she stakes herself.
Angel is so taken with his new son he won't allow anyone else to touch him. The Host comes to live at the hotel. Several groups are after baby -- demons, the vampire cult, gangsters, Wolfram & Hart -- and they all converge on the hotel and lay siege. The gang work a scam to get most of the baddies to destroy each other. Holtz recruits the twin sister of a vampire victim. Angel explains forcefully to Lilah's boss that any harm that comes to the baby will then also come to him, only moreso, whether or not he was the cause. The baby is named Connor.
At her birthday party, Cordelia suffers another vision. This throws her out of her body. The others thing she is in a coma. But she is being told by a messenger from the Powers that Be that the visions are killing her, and she will not survive the next one. She is offered the chance to be a famous actress, never having met up with Angel in LA. She accepts, but something drives her to investigate her last vision, and she finds a one-armed Wesley, and a broken Angel, fighting demons. She demands her visions and old life back. Her guide says that the only way that can happen is if she becomes part demon. She agrees, and wakes up healed. Then she has another vision, which doesn't hurt -- but she floats!
Angel is worried that he has to provide for Connor, so puts the firm on a more financially-oriented footing. Wesley and Gunn protect a woman being stalked by her dead boyfriend -- he's now a zombie, and it turns out she poisoned him in the first place. Some chrome-faced demons hire Fred to solve a puzzle for $50,000. A man promises Angel $10,000 to clean out a vampire nest -- but he has no money really, and is conning Angel to get his friends killers. Holtz continues in his search for humans wronged by vampires. Fred solves the puzzle, so the demons prepare to cut her head off. Cordelia has a vision of this, and the others arrive in the nick of time. Angel declares that family, and the Mission, are more important than money. But they earned the $50,000.
The gang goes off to see a ballet favorite of Angel's -- then he realises the cast is identical to when he last saw it, 110 years ago. They investigate, and experience some events that happened between cast members. Cordelia and Angel, in particular, are forced to act out some rather passionate past lives. They realise the whole production is trapped in a time warp due to a jealous lover. They free the cast, but not before Gunn is injured, and Fred declares her feelings for him. Angel is trying to declare his feelings for Cordelia when the Groosalugg reappears.
The Groosalugg defeats a demon in the sunlight, as a helpless Angel can only look on. Cordelia refashions Groo, but is worried she might lose her visions if she has sex with him. So she sends him and Angel off to get a magic potion to prevent that happening. Gunn and Fred are captured by a malevolent tree. Angel rescues them after Groo dashes in recklessly and gets speared. Angel sends the smitten Cordelia and Groo off with his blessing. Wesley deciphers a prophecy as "The Father will kill The Son"
Holtz's vampire killers infiltrate Angel's team, and set them up; Fred and Gunn are nearly killed by a vampire nest. Lilah steals some of Connor's blood. Wesley is concerned about the prophecy, and consults an beefburger oracle, who warns him the father will devour the son when there are three signs: and earthquake, fire, and blood. Sahjhan goes to Lilah for help killing Angel. Wesley goes to Holtz, and confronts him with Angel's goodness; Holtz is not impressed. The three signs occur...
Wesley takes Connor. Angel goes to find Lilah to discover what's happening. Sahjhan appears and tells Angel he's his mortal enemy, but Angel doesn't know him. Holtz attacks the hotel. Holtz' assistant tricks Wesley, slashes his throat, and takes the baby to Holtz. Sahjhan opens a portal to the deepest Hell dimension. In a four-way Mexican standoff between Lilah, Angel, Holtz, and Sahjhan, Holtz takes Connor through the portal.
Angel kidnaps the W&H's Special Projects boss, and makes him tell him how to make Sahjhan corporeal, so he can force him to open the portal again. Fred and Gunn discover Wesley's diaries, and the prophecy. They see Holtz' assistant Justine driving Wesley's car, and try to get her to tell them where Wesley is. She complains that Holtz betrayed her. A very solid Sahjhan appears, then Angel arrives. Sahjhan mocks them with how he changed the prophecies: the true prophecy was that Connor would kill Sahjhan. He starts beating them, but Justine traps him in a magic jar. Wesley turns up in hospital, badly hurt; Angel tries to kill him.
Seven years ago, Gunn traded his soul. Now the demon wants to cash in, and threatens to take Fred, too, if he doesn't come willingly. Cordelia and Groo return from their holiday. Gunn first breaks up with Fred, but she realises there must be a problem. It breaks Angel out of his black despair, and the gang go off to rescue Gunn. Wesley is released from hospital.
Cordelia is upset that Angel didn't call her when Connor was taken. Some transparent slugs are infesting the hotel, a result of the dark magic Angel performed to find Connor. When they take over a person, they dehydrate and kill them. Angel and co try to fight them, but one infests Fred. Gunn goes to an embittered Wesley for help. Angel talks to a slug through Fred -- they say the Destroyer is coming for Angel. Gunn forces Fred to drink alcohol; its dehydrating properties force the slug out of her. A slug attacks Cordelia, but she starts to glow, and banishes all the slugs. A large monster appears in the pentangle, then a teenager appears, kills it, and says "hello, Dad".
Connor is back from Hell dimension, calling himself Steven, and calling Holtz his father. He tries to kill Angel, and looks confused when Angel refuses to kill him. He runs off, and teams up with a drug addict, rescuing her from her pusher, cutting the pusher's ear off as a trophy. She tells him it's wrong to kill people, but when she dies from an overdose, he wants to track and kill the pusher. Back at the Hotel, Gru and Cordelia guard the rent to the Hell dimension. They kiss, and a bolt blasts them both unconscious. Something else may have come through. Lorne finds someone to seal the rent. Angel finds Connor, and Connor says he knows all about Angel, and how he killed Holtz' family, and how he is a vampire. Then and the pusher and his gang turn up, hot for vengeance, and then the police appear. In the ensuing fire-fight Angel saves Connor's life. A confused Connor departs, and goes back to a badly scarred Holtz.
Holtz makes Connor rejoin Angel. Cordelia gets a vision of a woman attacked by vampires in a bar, and Angel asks Connor to help him. The woman is Justine, and she's been set up by Lilah, as a test for Wesley. Angel and Connor save Justine, who then discovers Holtz is still alive. Holtz tells her he learned love in the Hell dimension, which destroyed his hate. Connor is rude to Lorne, and Cordelia explains that not all demons are bad in this dimension, why, even she is half demon! Connor then tries to kill he, but her powers instead wash all the toxicity from the Hell dimension out of him. Angel goes to confront Holtz. Holtz tells him that he is sending Connor back to Angel, and gives him a letter for Connor. Holtz then gets Justine to kill him, but when Connor sees the two stiletto holes in Holtz' neck, he just says " Angelus "...
Justine convinces Connor that Angel killed Holtz. Lilah continues her temptation of Wesley. Connor burns Holtz' body so he won't return as a vampire, then goes back to join Angel. Lorne says he is leaving. Groo tells Cordelia that she loves Angel, not him. Cordelia phones Angel and makes an assignation. On her way, she is stopped by Skip her demon guide, who says she is ready to ascend to a higher plane, and she ascends in a pillar of light. Connor meets Angel, and attacks him. Connor and Justine seal Angel in a steel coffin, and throw him in the sea. Fred and Gunn are left standing in an empty hotel, saying " where did everyone go? "