For three months Fred and Gunn have been searching for the vanished Angel and Cordelia. Wesley is with Lilah, saying he doesn't care what's happened to Angel, but he has secretly Justine captive, and knows what has happened. Eventually he finds Angel, rescues him, and takes him back to Fred and Gunn, telling them what Connor did, then walks away again. Angel tells Connor he loves him, and to get out. Lilah takes over at Wolfram and Hart. Still no-one knows what happened to Cordelia, but we see her surrounded by white light, bored.
The gang continue their search for Cordelia. Angel learns from Wesley that a powerful artefact can track her down, and tangles with Gwen, a thief with electrical powers who is stealing it for another client. In the struggle, she electrocutes Gunn, but pauses to revive him. Fred is devastated by Gunn's "death". Angel warns Lilah off Connor. Angel tracks Gwen and fights for the artefact. Then they are both trapped by the double-crossing client, who gases them. Angel doesn't breathe, so they escape, and he stops Gwen from killing the client. He uses the artefact to track Cordelia, realises she has ascended, and thinks that is the end of things. But we see Cordelia yelling get me out of here.
Cordelia begs Angel to rescue her, but he can't hear her. Angel needs direction in his life, so the gang go to Las Vegas, to see Lorne. But they discover he is being held captive, and forced to work for a mob stealing peoples' destinies. Angel's apocalyptic destiny is stolen, and he sits feeding quarters into a slot machine. Gunn and Fred are captured, and about to be killed, when a desperate Cordelia nudges Angel's machine, and makes him a winner. He gets taken to the boss, and has enough wit left to fight for his friends' safety. When they all return home, they find Cordelia at the hotel, but she doesn't recognise them. [Presumably she's been "exiled" for "tampering" with their lives?]
Cordelia has no memory, so the gang try not to frighten her with the truth. But she keeps discovering things, so they have to tell her. Lorne reads her when she sings, and runs off, shaken -- he's had a vision of the apocalypse. Connor rescues her from a demon, and they go off together. Wolfram and Hart attack, but it's a feint to draw the fighters away from Lorne. W&H suck his knowledge of Cordelia's future from him.
Fred learns her old professor was the one who sent her through the portal, and determines to kill him. Knowing Gunn is too sweet to help her (and that's what she loves about him), she enlists Wesley's aid. But Gunn, determined that Fred should not become a killer, kills him first.
Lorne comes up with a fool-proof spell to return Cordelia's memory. However, it leaves Cordelia, Fred, Gunn, Wesley and Angel with their memories up to the age of about 16, and Lorne unconscious. No-one knows what is going on, or who anyone else is. Angel is distressed to discover he is a vampire, and even more distressed when everyone attacks him. Connor arrives, and fights an Angel who is a sulky teenager ranting about his father. Eventually Lorne gets free and restores everyone's memory. The problem is, Cordelia now remembers everything.
Cordelia tells Angel that when she was a higher being, she saw Angel as Angelus, and felt how he enjoyed hurting people, and she now remembers that. Cordelia persuades Connor to go with her and follow her visions. They end up in the alley where Connor was born, and The Beast appears out of the ground. It is too strong for Connor to defeat. Angel persuades Lilah it is in her best interests to help them. The rest of the gang manage to track it to its lair, but it easily beats them. It disappears, and the sky starts raining fire. It seems like the end of the world, and so Cordelia and Connor make love -- but Angel sees them.
Connor goes to Lilah to try to discover his link to The Beast, but it appears there in the W&H building, and starts attacking and killing everyone. The building is "locked down", and Connor is trapped. Using a secret exit, Wesley rescues an injured Lilah, who tells him about Connor. The gang go to rescue him, but all the dead people have turned into zombies. They escape via the White Room -- where The Beast is sucking the dark essence from the little girl. Before she expires, she says the answer is among you, then sends them safely to the Hotel. Angel tells Cordelia to take her new boyfriend and go; she realises he knows.
The Beast is killing the Totems of Ra, as part of his plan to put out the sun. Gwen and Angel need to protect the last Totem from the Beast, but fail. The gang try to stop the Beast from completing the rite, but fail. Cordelia realises her vision of the Beast is a memory of him with Angelus in the past.
Wesley realises Angelus is needed to fight the Beast. He finds a shaman who can release the soul, then return it later. But the shaman makes to kill Angel. He's stopped, and found to be covered with writing that leads the gang to an underground cavern with a magic sword. There are several sappy speeches, and then Angel and Connor use the sword to kill the Beast, and the sun returns, and the whole gang are reunited. Cordelia and Angel start to make love. But then the whole story is revealed as a fantasy on Angel's part, brought about by the shaman to achieve a moment of perfect happiness, thereby releasing Angel's soul and restoring Angelus.
Angelus taunts all, and gets the gang fighting each other. Eventually Cordelia gets him to talk, by offering herself to him. He recounts the tale of his meeting with the Beast, and how the Beast was banished by a family of priestesses. The gang go to their descendents' house in LA, only to find the Beast got there first, and has butchered them all. They go to restore Angel's soul, but it is missing.
The gang hunt for Angel's soul, but can't find it. Lilah appears from her hiding place in the sewers, and is just stopped from freeing Angelus. Fred and Gunn split. Angelus tells Fred that Wesley and Lilah were together the past six months. Wesley discovers a spell has been used to remove all references to The Beast in this dimension. The gang learn The Beast has a Master. Cordelia has a vision of how to restore Angelus' soul, involving black magic. It appears to work, Lorne says his aura is back, but Angel gives a sappy speech, and asks to be left in the cage in case it is temporary. The rest leave, and Cordelia persuades him to come out. Then he reverts to Angelus, knocks her out, and escapes. The rest go off to kill him. But he doubles back, to hunt Cordelia and Lilah. Lilah says to Cordelia that Angelus will kill everyone. Cordelia stabs her, and says what do you think I let him out for?
Wesley has to decapitate Lilah's corpse, to ensure she hasn't been turned. Angelus finds The Beast, and taunts him for being a lackey. The Beast is then berated for mishandling Angelus by his Master -- Cordelia. Wesley realises they need Faith, so helps he break out of jail. The gang cast an anti-demon violence sanctuary spell on the Hotel. Angelus lures Faith to The Beast, who very nearly kills her. But then Angelus kills The Beast with his own bone knife. The sun is restored. Cordelia tells Connor they are having a baby.
Angelus is hearing The Master talking to him, and is defiant. Wesley and Faith track Angelus. Wesley is concerned that Faith has lost her dark murderous edge; she will need it against Angelus. Angelus comes back to the Hotel, to steal the books about The Beast. Connor attacks him, and falls foul of the anti-demon spell. The Master threatens to restore Angel's soul if Angelus disobeys him. Faith and Angelus fight, and Angelus bites Faith.
Faith has spiked her blood with the magical drug Orpheus, and now both she and Angelus are in a coma, having linked flashbacks to Angel's life. Willow arrives, called by Fred to help re-ensoul Angel. Willow and Cordelia bring each other up to date: "Higher being." "Ultimate Evil." Lorne says Faith is dying from the drug. Cordelia tries desperately to stop Willow breaking the jar containing Angel's soul, and when she fails, sends Connor to kill Angelus. But Faith, revived by Angel's dream-lecturing, awakens, and stops Connor. Willow's spell works, and Angel reappears. Cordelia announces her pregnancy to all.
Gwen asks for Gunn's help rescuing a kidnapped little girl. But she's actually trying to steal a device that might cure her weirdness. The device works, and Gunn can touch her. Connor asks Cordelia why she tried to get him to kill Angelus. Angel tries to remember the book about the Beast that Angelus destroyed. Lorne engages in a ceremony to regain his power to read people. Cordelia tries to kill him before he can expose her, but it's a trap, and the gang catch her in the act.
Connor rescues Cordelia from the gang, and she says they were going to kill her because they fear her baby. Angel goes to find Skip, to discover just when the Beast's Master took over Cordelia -- he finds Skip was in on a long-standing plot, for the Master to create a vessel it could inhabit: Connor's child. Skip tells the gang the only way to stop the evil is to kill Cordelia -- and even if the baby is born, it will suck her life force. Cordelia gets Connor to capture an innocent for a birthing rite. Darla returns, to try to persuade Connor not to do it, but Cordelia out-argues her. The woman is sacrificed, and the birthing begins. Angel arrives to kill Cordelia, but just too late. A fully-grown woman is born, and Angel and Connor fall to their knees in worship.
Cordelia is comatose, but her daughter is worshiped by all who see her, and preaches a message of love and good will. She helps the gang destroy bands of monsters. But then Fred sees her true form -- an horrific monster. She can't convince the rest of the crew that she's telling the truth. They decide she is evil, and must be killed. She runs off, into an LA besotted with their new god.
Fred is on the run, and Jasmine's connection to all "her" people means everyone's after Fred. Meanwhile, LA is reverting to a peaceful sunny 1950s style existence. After a run-in with a flesh-eating demon, Fred realises that she can see Jasmine's true form because their blood mingled. She shoots a bullet through Jasmine into Angel, and now he's infected too. Jasmine realises about the effect or her blood. Connor discovers she is "eating" her followers, but is unmoved. Fred and Angel wonder how to get more of Jasmine's blood, then Angel realises the comatose Cordelia's might be sufficient. It is to return Lorne, Wesley, and Gunn. But it has no effect on Connor, and he gives them away to Jasmine.
The gang go into the sewers to evade Jasmine, and meet up with a gang of kids forced down there by the vampires when the sun was out. Jasmine removes Cordelia to a safe place. The gang discover an insectoidal monster in the sewers, from another dimension where Jasmine loved them first. They discover Jasmine's true name will break her power. Angel goes the the Hell dimension to find the name, whilst the others try to battle of Jasmine's forces.
The gang are caught by Jasmine's forces, and locked in the basement cage. The blood had no effect on Connor because he always knew Jasmine's true form, but wanted to believe anyway. Connor discovers where Cordelia has been hidden. Angel finds the Keeper of the Name, and returns in time to break Jasmine's spell, plunging the world into chaos and violence. Jasmine's main power has been broken, but she still has enough to threaten the world. Jasmine accuses Angel of having destroyed the chance for peace, but he maintains it is meaningless without choice. Connor kills her, and walks away, defeated. Lilah returns, saying Angel has destroyed world peace.