The episode starts with Buffy in the cemetery having a hard time fighting a single vampire, with Xander, Willow, and Anya there to help. A second vampire attacks her. They succeed in slaying the first one while the second one escapes. They follow it back to its hideout, in a crypt, where they find a nest of five vampires feeding on a dead victim.
"I don't care if it is an orgy of death, there's still such a thing as a napkin," Willow says, as they exit the crypt. Buffy thinks she could probably handle them, but the others don't think so they decide they need help.
In a large, white mansion they enter a high ceiling study and approach an oak desk. Buffy is timid when she says there's a problem. The tall leather chair swings around to face them to reveal a suave young man Jonathan. "Sounds like you can use my help," he says, with a confident smile.
In Giles' apartment, Jonathan and the gang are readying themselves to attack the vampire nest. Willow, on her laptop, is frustrated when she can't find another entrance into the crypt. Buffy tries to tell them her plan to lure the vampires out, but Jonathan makes a suggestion and Buffy's words are ignored. As they leave, Jonathan moves a pawn on the chessboard of his and Giles' current game that will have him in checkmate in four moves.
Back at the crypt, Buffy shoots one of the vamps with her crossbow. As the other four stand up, Jonathan drops down through the skylight, armed with an automatic crossbow, and takes out two of them. Buffy stakes a fourth and Jonathan shoots the fifth, one that got by Buffy.
Buffy pouts that she let a vampire get by; Jonathan gives her a pep talk, saying she did her best. Buffy, though, isn't convinced that it was her best. As the gang follows Jonathan out, they find a group of paparazzi waiting for him. He pauses for a second as they snap shots of him, and then breaks them up. The gang is raves about their success at the nest, saying that Buffy would have been killed if she had tried it alone. Jonathan is giving them a lecture about vampires when he senses a lurking Spike in the shadows.
"Well, well. The Man himself," Spike says, as they size each other up. Spike hardly notices Buffy, calling her "Betty." It seems Jonathan knows all about Spike's implant and warns the vampire that if he finds a way to turn back to normal he'll soon find himself looking like "instant soup mix."
Later, Willow is recounting the nest attack to Tara as they tape clippings of Jonathan on the wall. Tara asks about Buffy and how she's dealing with Faith (in Buffy's body) having slept with Riley. Willow thinks they're probably making with the smoochies right now.
They're not. In Riley's room, Buffy comments that he seems to be healing from his Adam-donated wound. He's no Jonathan, he says, and tells her the Initiative swears they've stopped drugging the commandos' food, though he's not sure he trusts them. Riley's still not sure if, without the drugs, he'll become weaker, dumber, or smarter. The Initiative has so far failed to find Adam and refused to release his whole profile; Riley wishes they trusted him enough to let him get the job done. Buffy knows how he feels. When Riley tries to get close to her, Buffy becomes uncomfortable and leaves.
The next day, Buffy shares her problems with Jonathan, buying (and preparing) him a cup of coffee at the Espresso Pump. Buffy blames Faith for messing things up with Riley, but Jonathan suggests maybe she's actually angry at Riley, for not realizing that she wasn't herself. Jonathan encourages her to forgive him. An excited fan, Karen (with a "K") comes up to Jonathan and he signs her copy of his autobiography Oh, Jonathan. She goes away in a joygasm. Buffy wants to know how she can get past her resentment. He tells her it's not gonna be easy, but what she and Riley have is special and worth the hard work to get through it. Buffy's still not sure how to make everything okay, and Jonathan knowingly tells her, "If you really want it, you can make anything happen."
Back at the Initiative, there's a new man in charge, Colonel George Haviland. He's debriefing Riley and the commandos on their mission to recover Adam. He then turns the debriefing over to their tactical consultant Jonathan. "About time they brought out the big guns," Graham whispers to Riley. Jonathan proceeds to tell them that Adam doesn't need to eat, as he has an unlimited supply of power in the form of uranium located within his spinal column. Because of this, Jonathan reasons, Adam will need to be completely destroyed in order to be killed.
Meanwhile, on Jonathan's property, Karen is standing in the rain trying to peek inside his mansion using a pair of binoculars. Just as she complains that he's never home, she's attacked by a monster with a strange symbol on its forehead. After suffering some scratches and bruises, she manages to escape.
At the Initiative, Riley seeks advice from Jonathan about his relationship with Buffy. Jonathan tells him she's ready to forget and move on, she's just worried that he'll compare her to Faith, considering Faith's sexual experience. Riley thinks that Buffy knows he wouldn't do that, but Jonathan encourages him to let Buffy know that she's the only one for him.
Later, at the Bronze, there's a swinging jazz band on stage. Buffy, Riley, Xander, Anya, Willow, and Tara are all there. Xander is upset with Anya, accusing her of calling out Jonathan's name during an intimate moment. Anya explains it was just a moan. Buffy and Riley observe the couple, and a gloomy Buffy comments, "They get into a fist-fight, I got a fifty on Anya." Suddenly, Jonathan appears on stage, dedicating the next song to them, and begins to sing a soft ballad. Riley asks Buffy to dance and leads her out on the floor. She holds him tight and when he tries to apologize and tell her how much she means to him, she stops him, saying she already knows. Enjoying the moment, he put his arms around her.
Tara becomes excited when Jonathan leads the band into the next song with a trumpet solo, as she realizes that he's performing a song from his new album. A dreamy eyed Anya tells Xander "Let's go have sex now." Xander agrees and the duo exit. Enter a frightened Karen. Buffy asks her if she's okay but she heads straight for Jonathan. He stops the band and gently asks her to tell him what happened.
The police are waiting at Jonathan's mansion, arousing Buffy's curiosity. The sergeant barely looks at her and informs Jonathan that they received a call that there was a disturbance on the property so they came to check and make sure he was all right. Jonathan assures him that he has everything under control and the police leave. Karen describes the creature and remembers that it had a symbol on its forehead; she draws it for him. Seeing the symbol, Jonathan tells them that it's just a monster that was probably more afraid of Karen than she was of it. Buffy wants to patrol anyway, but Jonathan assures her he can handle it himself. Buffy is a little uneasy.
In a library somewhere, Adam is sitting at a desk in front of several monitors, reading; the dead librarian looking a dead only Adam is capable of. When he sees Jonathan on all the channels in the monitors, he realizes the world has been altered. The vamp flunky with him comments that the world feels normal to him. Adam explains that the vamp, along with everyone in the world, is under a spell. Adam wasn't affected because he is aware of every molecule in his body, more "awake and alive" than anyone on the planet. Adam decides to do nothing about Jonathan since this kind of unstable magic will ultimately lead to chaos, which he has an interest in.
Jonathan is standing in front of his lit fireplace, alone in his dark study. From the balcony on the second floor two lingerie-clad blondes (Swedish twins) call down to him to come to bed. He says he'll be right there. He removes his robe and we see a symbol on the back of his shoulder the same one on the monster's forehead.
Buffy, Willow, and Tara walk across campus back to their dorms. Willow expects they'll have to go out hunting for the monster, but Buffy tells her Jonathan was going to take care of it. Buffy thinks Jonathan might have been a little scared. Willow reminds her that he doesn't get scared Buffy herself talked about it when she presented him with the Class Protector award at the prom. Tara heads off to her room and finds herself alone in the empty corridors. The monster suddenly bursts from out of a door and attacks her. A terrified Tara escapes by using a clouding spell and locks herself in the janitor's closet. The next morning Buffy arrives at Tara's room where Willow is taking care of her. Apparently, Tara spent the entire night in the closet and was found only an hour ago. They realize that she was attacked by the symbol-wearing monster, which confuses Willow, as Jonathan had told them they were all safe from it.
A thoughtful Buffy wanders around town looking at all the posters, billboards, and advertisements with Jonathan's face everywhere. She goes to Xander's basement where she finds only Anya, but she just wants to look at some of his stuff. She finds comic books, trading cards, and posters, all about Jonathan. Anya, uncomfortable with Buffy's presence, is reading Jonathan's autobiography, right at the part where he invents the Internet. Buffy starts asking her questions about her demon days, how she use to grant wishes to punish men, and wonders if someone could change the whole world. Anya tells her that alternate realities are indeed possible.
That night, everyone gathers at Giles' place and Buffy tells them her idea that maybe Jonathan is too perfect. Her evidence includes the fact Jonathan went to medical school before graduating from high school, and also starred in "The Matrix" without ever leaving town. The gang refuses to believe this after all, Jonathan was the one who smashed the Master's bones to dust and blew up the mayor during graduation, the one who lead the US women's soccer team to a stunning world cup victory and they all saw him do these things. Buffy tries to convince them that maybe they shouldn't trust their memories, but Giles feels she's out of her depth. Even Riley says it sounds like nonsense, but follows by saying that Buffy seems to see things differently than everyone else and, for once, they should follow her lead. Looking for proof, Buffy asks Giles if he has a Jonathan swimsuit calendar and is surprised when he says he doesn't. Embarrassed, he admits he does, but insists that it was a gift. Buffy flips to the month that shows Jonathan's shoulder, with the symbol on it. Suddenly, Jonathan suddenly appears at the front door and explains to the gang that he does have a history with the monster. Every time he's faced it, his mind gets confused and he has difficulty fighting it, which his why he wears its mark, as a reminder not to underestimate it. Everyone but Buffy is relieved; she suggests that she and Jonathan try to find the beast.
On the way, they run into Spike again at the cemetery and he comments that Jonathan's taking the sidekick out for a walk. Buffy doesn't back down from him, but she doesn't try to stop him as he caresses her hair, face, and almost her chest. Jonathan steps in and slams him against a crypt, demanding to know if he knows where the monster might be. Spike proves uncooperative and Jonathan turns to leave, but Buffy slams Spike against the wall again. Spike is shocked by Buffy's surprising display of power, and she succeeds in getting the information. Buffy's tactics have impressed Jonathan, and she beams with pride.
At Giles' apartment, the rest of the gang find out the symbol is a part of an augmentation spell, which changed Jonathan into a paragon the best of everything, everyone's ideal. However, in order to even the balance between good and evil, it also created a monster of equal evil, everyone's worse nightmare. (Xander thinks it's so cool that Jonathan would use a spell to make the whole world think he's so cool.) The gang determines that if the monster is killed,the spell will be broken, and Jonathan will revert back to what he was. Anya figures that in that case, Jonathan won't want Buffy to find the creature.
Jonathan and Buffy explore a cave, where they find a seemingly bottomless pit. They're about to continue searching for the monster when it suddenly jumps out at them and knocks Jonathan out.
At Giles', everyone is quite surprised to realize that Buffy was right. But they're also concerned about what would happen if Buffy actually killed the creature, how would the world change. Giles explains that the only thing that would change is Jonathan; everything else is real. They wonder if Buffy can even succeed, as she's never faced anything this big on her own.
Jonathan regains consciousness to find Buffy getting knocked around by the monster. He gets up and starts beating the crap out of it but it doesn't look as if he can hurt it himself. Buffy begs Jonathan to tell her what to do, but he says she's gonna have to handle this one solo, like she used to. She's scared by this but takes the creature down when it charges her. In fear, Jonathan suddenly runs for cover as Buffy proceeds to beat the monster, her confidence growing. The creature knocks her down and Jonathan steps out into the open, brave again. Buffy gets back up and counterattacks; Jonathan ducks for cover once more. The monster knocks Buffy down at the edge of the pit and it's about to throw her in when Jonathan tackles it and they both fall in. Buffy grabs Jonathan's foot and saves him.
All over Sunnydale (and the world) everything turns back to normal; all things Jonathan disappearing.
The next day on campus, Buffy and the gang are talking about what had happened and how it all seemed so real. Xander seems the most upset. "Poor Xander," Buffy says, "I guess Jonathan hurt you most of all." A battered Tara raises her hand. "Except, of course, after Tara." Buffy sees Jonathan and walks over to him, as Anya wonders, "Who really did star in The Matrix?"
Jonathan tells Buffy that everybody seems to be forgetting what happened, himself included, and some are angry. He explains that during group counseling after his suicide attempt, he met a kid with a spell the kid didn't warn him about the evil monster part. Buffy reasons that people are angry because they didn't like being sock puppets in his world. Jonathan understands, but explains that he just wanted friends. Buffy sees his side as well, but advises him that making friends is complicated and takes time and hard work. He agrees. As he's about to leave, Jonathan asks if she remembers the advice he gave her about her and Riley. Though he doesn't remember the details of it, he thinks it was right, and probably the same advice she just gave him. Buffy confirms that she does remember.
That night, in Riley's room, he and Buffy are kissing. Buffy's glad they talked things out, but Riley points out they haven't talked at all. Buffy likes what they're doing anyway, and the two start kissing again. Buffy lets out a moan "Jonathan."
Synopsis written by Joseph B.