Buffy is having a hard time adjusting to college -- but Willow and Oz think it's great. When Buffy gets beaten up by a strong vampire, she goes to Giles for help, but he tells her she can handle it herself. She goes home, where she gets an anonymous phone call. She finds that her mother has filled her room with packing cases. She meets Xander in The Bronze, and he restores her confidence. They research the vampire, and find its lair. Xander goes to get her weapons while Buffy watches. But she is discovered, and has to fight the vampire. Xander, Willow and Oz arrive to help her with the others. Giles also arrives to help, but only after all the vampires are dust.
Buffy grows increasingly irritated with her roommate Kathy: her music, her tidiness, her labelled milk. And this seems to grow into an obsession after an encounter with a demon, and terrifying nightmares of a ritual involving scorpions and forced ingestion of blood. Finally she claims Kathy's toenail clippings keep growing, that Kathy is evil, and she will have to kill her. The rest of the gang are worried how Buffy is acting out of character, and confine her. Then Giles discovers Buffy is actually right, and that Kathy is slowly sucking away her soul, so that she herself will not be recognised as a soulless demon. Buffy escapes and goes to confront Kathy. Giles and Willow cast a spell to restore Buffy's soul, and when the Big Demon arrives, he takes Kathy, the soulless one. Willow moves in to become Buffy's new roommate.
Willow meets an old classmate, Harmony, one of the "Cordettes", who is now a vampire. In fact, she is teamed up with a returned Spike (who calls her "Harm"). He is searching for a magical ring that makes vampires invulnerable. Buffy has an affair with Parker, but then he brushes her off. "Is this the way it's always going to be? I sleep with a man; he turns evil?" Spike eventually finds the ring, and attacks Buffy in broad daylight. She only just manages to beat him, and takes the ring. He has to flee, burning. Buffy decides to give the ring to Angel, and Oz offers to take it to LA.
Buffy, moping over Parker, reluctantly joins Willow, Xander and Oz at a frat-house Halloween party. But unknown to them a demon-summoning spell has been cast, and they are soon trapped in a real-life house of horrors, tormented by their own worst nightmares. Anya realises there is a problem, and contacts Giles. He fights his way into the house with a chainsaw. Buffy accidentally completes the spell, and the demon materialises. But it is only six-inches high, and Buffy stomps it.
Buffy fantasises about rescuing a grateful Parker from vampires. She tries to drown her sorrows by sharing a few beers with three students, at Xander's new workplace. But the beer has been spiked by the disgruntled bar-owner, and reverts them to Cro Magnons. Willow confronts Parker about his treatment of Buffy. He tries his charm on her, but she is not that gullible. The Cro Magnon guys start a fire, and Cro Magnon-Buffy, Willow and Parker are trapped. Buffy rescues them, and a grateful Parker tries to apologise. She clocks him.
Spike is abducted by the "commandos". Oz is still attracted to the mysterious new singer Veruca. Willow tries to control her jealousy. Then, on the night before the full moon, having broken out of his cage, he discovers she's a werewolf, too, but that she roams wild. The next night, he cages her with himself, and Willow discovers them both in the morning. She is devastated, and starts to concoct a revenge spell -- but she can't go through with it. Buffy and Oz are out hunting Veruca in the woods, and discover she is hiding her tracks. Buffy collides with a commando in the woods. They realise Veruca is after Willow, and rush back. Veruca confronts Willow, but Oz rushes in, and, turning into werewolf mode, kills Veruca. Buffy tranquilises him before he can get to Willow. Oz decides he has to go off to confront the animal in himself, leaving behind a distraught Willow.
Willow is upset that Oz's name has been removed from the Professor Walsh's class list, and Buffy upbraids Walsh for not being more sympathetic. Riley decides he is interested in Buffy after he hits Parker for making a nasty crack about her. Spike, captured by the commandos and locked in an white underground cell, manages to escape. He thinks this is Buffy's doing, and sets out to kill her. He captures Willow, but is unable to kill her. Professor Walsh is the head of the commandos, and Riley her chief lieutenant. She sends them out to recapture Spike, but Buffy gets caught up in the fight, trying to save Willow, and Spike escapes. We learn he has an implant that makes him unable to kill.
Despite the non-PC aspects of the celebration, Buffy's determines to host a Thanksgiving at Giles'. But then Xander falls into the ruins of a lost Sunnydale mission, freeing the vengeful spirit of a Native American tribe. Angel shows up in the shadows, having been warned Buffy is in trouble. Spike come round to Giles, to tell Buffy about the commandos -- yet for some strange reason she doesn't trust him. Then the Indian, with a group of followers, attacks. They have Buffy and Giles, and a bound Spike, surrounded and badly outnumbered. Spike can't dodge the arrows, and looks like a pin-cushion. Then the cavalry arrives -- on bicycles, and the attack is defeated. Angel manages to help without ever being seen by Buffy, but Xander lets the cat out of the bag at the end.
Still depressed about Oz, especially as he sends for his things but leaves no message for her, Willow casts a spell to have her will done -- so she can will herself better. It apparently doesn't work, but when she lashes out at those around her, it does: she says Giles "can't see anything", and he goes blind; Xander becomes a demon magnet; Buffy and Spike fall in love start planning their wedding. Riley is devastated when Buffy tells him the good news. The demon D'Hoffryn is delighted with the side-effects, and offers to make Willow a vengeance demon, just like he did Anya a millennium ago. Willow is horrified, turns him down, and gets sent into the middle of a big fight against the demons Xander has attracted. She reverses the spell, the demons run off, and Spike and Buffy are disgusted to find themselves kissing each other. Buffy convinces Riley she was joking -- he now thinks she's mad, but at least she's free.
Buffy notices that whenever she and Riley get close, she starts babbling, then he starts babbling, and nothing happens. Willow joins a Wicca circle, but is disappointed to discover they aren't real witches. Then "The Gentlemen", a group of fairy-tale demons, steal the voices of everyone in Sunnydale. They do this so that they can steal the hearts of their victims without any screaming. Buffy and Riley manage their first kiss in the ensuing silence. Giles discovers what the demons are from a book of fairy tales -- and that "the scream of the princess" will destroy them. Buffy goes on patrol; Prof Walsh sends her commandos out to keep order. Tara, a very shy member of the Wicca circle, and the only other one in it with any powers, is trying to find Willow for help, when the demons start chasing her. She and Willow end up trapped, but join forces, and save themselves from the demons. Tara is very taken with Willow's powers, and says her own mother was a powerful witch. Buffy and Riley independently track the demons to their lair, and join forces to fight them. Riley breaks the box holding all the voices, and Buffy screams to destroy the demons. Buffy and Riley decide they must talk, but just sit in silence.
Buffy and Riley decide to confess to each other, although Riley has never heard of The Slayer. An earthquake heralds the reopening of The Hellmouth, and three demons are determined to bring about the apocalypse. So it's back to high school, to stop them. Buffy tries to convince Riley she isn't interested in him -- really because she's afraid he will get hurt. A depressed Spike tries, but fails, to stake himself, and a concerned Willow insists he joins them in their demon fight. Riley turns up, and helps Buffy stop the final demon from completing the ritual. In the melee, Spike discovers he can fight demons, and is overjoyed, and wants to carry on fighting them, immediately!
Buffy tells Prof Walsh she is The Slayer; Riley is astounded by her kill total, and by her strength. Giles feels left out when he discovers he is the only one who didn't know Riley is in the Initiative, and when Buffy unintentionally insults him at her 19th birthday party. Then he gets turned into a demon. Buffy is convinced the demon has killed Giles, and tracks him down intent on killing him.
Prof Walsh welcomes Buffy the Initiative. She even gives her a beeper. Willow is feeling left out as Buffy spends more time with Riley, and Xander with Anya. So Willow spends more time with Tara. In the secret room 314 Walsh is building "Adam" out of demon parts. Spike has moved into a crypt of his own, and wants to cut all ties, but when he is spotted and tagged by the Initiative, has to go back to Giles for help. Walsh discovers that Buffy knows something about 314, so gives her a broken gun and sets her up to be killed by two demons. But Buffy makes mincemeat of them. Riley discovers Walsh's perfidy, and walks out. Then Walsh is stabbed by a surprisingly awake Adam.
Riley's world is falling apart from discovering Walsh tried to have Buffy killed. He is also suffering withdrawal symptoms from the drugs that were in his food to make him strong. Adam has escaped, and killed a child. Buffy is determined to kill this monster. Riley is confused when he finds the escaped Hostile, Spike, at Giles', and Buffy "consorting" with demons at Freddy's Place as she tries to track down the monster. Willow casts a demon-locating spell, but Tara sabotages it. Buffy, Xander and Riley confront Adam in the lab; he is so strong he easily beats them all and escapes. Some demons beat up Spike for working with The Slayer.
After 8 months in a coma, Faith wakes, and escapes the hospital. Riley joins Buffy to hunt Adam, but with no success. The mayor has left Faith a strange device. When Faith attacks Joyce, Buffy comes to her mother's rescue, but in the final fight, Faith uses the mayor's device to swap bodies with Buffy.
Faith-as-Buffy behaves badly with Buffy's friends -- but Tara, meeting her for the first time, realises there is something wrong. Buffy-as-Faith is kidnapped by the Watcher's Council, who decide she is too much trouble to take back to England, and attempt to kill her, but she escapes. Meanwhile Adam contacts a group of vampires, and persuades them to confront their biggest fear -- so they a take a churchful of hostages. Faith-as-Buffy feels compelled to help, and she and Buffy-as-Faith save the congregation, then fight, during which they swap bodies back. Faith runs off. Buffy is distraught to learn that Riley slept with Faith-as-Buffy.
Jonathan, who nearly committed suicide, is here the hero, a famous Jazz trumpeter, the star of The Matrix, a James Bond style demon-killer, a dot-com guru, a swimsuit calender model, adored by everyone: he's even in the episode credits! But Buffy senses something is wrong, despite the fact that he has given both her and Riley sage advice so they can get back together after Faith's deceit. Jonathan has cast a spell to make himself a superstar, but there's an evil monster mirroring him. Buffy realises in time what's going on, and destroys the monster, thereby cancelling the spell.
Adam has demons and vampires working together. Buffy and Riley get very close, which leads to strange goings-on at Riley's fraternity house's party. Everyone is very sexually charged. Giles, after singing in a cafe, discovers the house used to be a repressive children's home, and Buffy and Riley's energy has loosed a lot of bad karma, haunting everyone, and draining the pair. Xander and Anya brave the ghosts to rescue their friends.
Oz returns to Sunnydale, with the "wolf" under control, after lessons in Tibet. He wants to try again with Willow. Riley is shocked to learn Oz is a werewolf. Willow tells Buffy how she feels about Tara. Oz smells Willow on Tara, and loses control. But before he can hurt her, is is captured by the Initiative. When Riley realises the wolf is Oz, he tries to free him, but is himself captured and detained for court martial. The gang, aided by Spike, who is now in cahoots with Adam, rescue them both. Oz realises he must leave, and Willow returns to Tara.
Adam gets Spike to drive a wedge between Buffy and the gang, by casually passing on false gossip. Angel turns up, to apologise to Buffy for they way he spoke to her in LA, and ends up fighting with Riley. Buffy and Forest discover Adam in a cave; in the ensuing fight Forest is killed, and Buffy barely escapes. Buffy tells Riley, but then he starts acting strangely, and goes to meet Adam...
Using a chip implanted by Prof Walsh, Adam gains control of Riley. He plans to lure Buffy into the Initiative, so that she, the soldiers, and the monsters can all kill each other, leaving Adam body parts to make an army of zombies. But Buffy has discovered Spike's deception, and the Scooby Gang is together again, helping her. Willow decrypts the discs Spike stole, and they all realise it's a trap. So they cast a spell that makes Buffy powerful enough to overcome even Adam. Riley rips the chip out of his chest, and even Spike joins in the final fight on the side of the good guys. The government decide the Initiative experiment has failed, and shut it down.
The gang get together at Buffy's to relax after the show-down with Adam, but the spell they cast has awakened the old power of the First Slayer. They each have disturbing dreams, which threaten to kill them unless they can recognise and defeat her. Might the cheese be a clue?