While Buffy visits an empty Sunnydale High School, Riley wonders why he has paid a visit to Adam's lair. While referring to Riley as his brother, Adam explains that Professor Walsh implanted a behavior modification chip in Riley's central nervous system, and that he has activated to carry out his 'plan.' When Riley professes his intent to stop Adam, Adam tells Riley to sit, and Riley dutifully carries out his order. Adam continues to explain that Professor Walsh planned for Adam and Riley to be part of a master race that is better than both demons and humans. Spike makes an uninvited entrance, demanding the chip be removed from his head. Adam tells him that he must draw Buffy into the Initiative before he has met his part of the bargain. His plan is to have Buffy kill as many demons as possible before he kills her. Riley tries to voice his real opinion, but is quickly silenced by the behavior chip when Adam orders him to stop talking. When Spike realizes that there might be a hole in his plan to separate the Scooby Gang, he leaves Adam's lair to correct the situation. Willow and Tara stop by Giles' house to pick up her laptop and the disks, and Willow shares an awkward moment with a hung-over Giles. With the previous night's events, none of them know what to say, and their exchange seems like the beginning of a long goodbye.
Buffy sits alone in her dorm room, thinking about the night before. She gets up and finds an old picture of Willow, Xander and herself, and has a quiet moment of reflection before assembling her weapons for the battle to come. Over in Xander's basement, Anya arrives to find Xander still lying in bed. Xander won't go to the unemployment office because he has been thinking about what Buffy and Willow had said the night before, and he is coming to believe that he is a loser with no future. Anya lies down beside him and tells him that no matter what his friends think of him, she still loves him. Buffy returns to the cave where Adam killed Forrest and finds Adam's lair, but Adam is not there. Adam, meanwhile, leads Riley into a secret area of the Initiative where he says the new race will begin. He tells Riley that Professor Walsh hid her secrets very well. Riley is shocked to see a scared, but re-animated Professor Walsh limp over to assist a re-animated Dr. Angleman operate on a body in the corner of the vast underground space. Realizing that Adam has killed Walsh and Angleman as part of his plan, he fears that Adam has the same planned for him. Just as Adam assures Riley that his fate is much greater than Walsh's and Angleman's, Forrest sits up from the operating table, brought back to life with a face made partly of yellow demon skin.
Still patrolling the caves, Buffy runs into Spike, who inquires about the information on the disks that he gave to Willow. When Buffy tells him that they haven't been decoded, Spike tells her that even though they have had a falling out, they should still concentrate on decoding the disks. Knowing that Spike wasn't around to see their "falling out," Buffy begins to put things together. Just as Buffy begins to realize Spike's plan, Willow gets closer to decoding the disks in Tara's dorm room. Just before Willow has figured out how to break the code, the disks begin decoding themselves, spitting out information about the Room 314 Objective. As the disks decode, Buffy calls on the phone. Soon after, Buffy, Willow, Giles and Xander all meet in the middle of campus. Buffy explains to them that Spike instigated their battle of words by spreading rumors to each one of them individually. While they all realize that Spike had tricked them into their squabble, the doubts about the strength of their friendship remain. After an uncomfortable moment of silence, Buffy figures out that Adam was planning on releasing demons in the Initiative to kill the soldiers, then using Spike to lure her in to kill the demons, leaving him with hundreds of parts with which to build his new race of human-demon hybrids. When Xander asks if Adam is worried that Buffy will get in the way of his plan, Buffy realizes for the first time that Adam may be too powerful to fear her.
Back in the secret Initiative lab, Riley sits bound in a chair, while Professor Walsh prepares him for his 'operation.' When he tries to talk to her, Forrest informs Riley that she is merely a walking corpse, but that he is more alive than he has ever been, and that Riley will be joining them soon. As Riley tries to tell him that they will never control him, Professor Walsh injects him with a clear liquid. Back at Giles' house, Buffy, Willow, Xander and Giles try to figure out how to defeat Adam. Willow suggests casting a spell to paralyze Adam, but the spell must be recited in Sumerian by an accomplished wicca in close proximity to the subject. Xander sarcastically surmises that they need someone with the strength and speed of Buffy, the magic expertise of Willow, and the linguistic skills of Giles. To Xander's surprise, Giles tells him that's exactly what they need. While they break into the Initiative house, Giles explains to Buffy, Xander and Willow that while an "enjoining" spell is powerful enough to defeat Adam, it is also very dangerous.
As Buffy and Willow rappel down the elevator shaft into the Initiative compound, Buffy apologizes to Willow for what she had said. She tells Willow that she has been too wrapped up in her own life lately to be a good friend. Willow apologizes for keeping Tara a secret from Buffy and everybody else, and as the two embrace, they fall to bottom of the shaft. Xander follows them down, and when he lands, they gleefully embrace Xander, and tell him that they missed him. For the first time in a long while, the Scooby Gang is happy to be together, and ready to do battle. But when they pry the doors to the initiative open, they are greeted by a bevy of soldiers wielding guns. Adam and Spike watch Buffy and the gang being escorted through the halls by Initiative soldiers on closed circuit TV. When Adam sees that Buffy's friends are still with her, he orders Forrest to honor his agreement with Spike to remove the chip by tearing off his head. Spike puts his cigarette out in Forrest's eye, and narrowly escapes a gruesome death.
In the Initiative control room, Buffy tries to tell Colonel MacNamara that Adam is planning an attack from within his own compound, from a secret lab built for the 314 Project. Unaware of any of these activities, the Colonel tells her that every inch of the compound is under surveillance, and that a tic couldn't get in without him knowing about it. Just as he professes his control over the situation, the power goes out, and a soldier at the controls informs everyone that backup generators are not responding, locking them all in the compound. From his secret control room, Adam opens the containment units, and the demons immediately pounce on two unlucky Initiative doctors. Buffy urges the Colonel to let her go and escape with his men, but he orders his men to take the infirmary and leaves two men to keep Buffy and the Scooby Gang under arrest. Buffy immediately dispenses of the two soldiers, and Willow takes the reigns at the control console. As they look into the monitor, they see the fierce battle going on throughout the Initiative compound. Blood and carnage are everywhere as the demons massacre the doctors and soldiers. Amidst the melee, Spike suddenly returns to his old self, the behavior chip somehow disabled. In a flash of fury, Spike manhandles a small battalion of demons en route to his escape from the compound. Back in the contol room, Willow uses the schematics of the compound to try and find a way out. Instead she finds a system of air ducts that supposedly lead to nowhere. Buffy speculates that the air ducts must lead to Adam's secret lab, so the Scooby gang sets out to find it.
Armed with only stun gun, Buffy, Xander, Willow and Giles run through the main operations room of the Initiative, knocking demons out of their way right and left. Willow narrowly misses being shot by a panicking Initiative soldier, and Xander saves Buffy by blasting a demon with the stun gun. Miraculously, they make it through the explosive battle unscathed, and enter into a small laboratory. They move a cabinet in the corner to reveal a secret door that leads to Adam's secret lab. Buffy pauses at the door and tells Willow to barricade the door behind her. Xander tells Buffy that he is still uneasy about Buffy going in alone, but Buffy assures him that with the magic spell, she will not be going in alone. With that, Buffy goes in, and Willow barricades the door. When Buffy enters the secret lab, she finds Riley bound in his chair. She asks Riley to tell her what is going on, but he is unable to speak. Adam comes out from the shadows and orders Forrest, Professor Walsh and Dr. Angleman to kill Buffy. Forrest grabs Buffy from behind and Walsh approaches with a medical saw.
In the other room, Willow, Xander and Giles perform the enjoining spell as Buffy breaks free from Forrest and sends Professor Walsh to the floor with a swift kick. Buffy tries to take Forrest out, but Adam has made him too powerful and he throws her to the floor, breaking a bottle on the arm of Riley's chair. As Forrest wails on Buffy, Riley grabs a piece of the glass and cuts into his chest, painfully beginning to remove the behavior modification chip. As the spell in the other room progresses, Buffy gains some momentum, which is quickly crushed by Forrest, who slams her down onto an operating table and holds her down. On her way down, she breaks an electric cable coming down from the ceiling. As Walsh and Angleman approach Buffy, Riley rips the behavior chip from his body and gets up and tears the life-giving tubes from Walsh and Angleman, sending them to the floor, dead once again. Riley begins his rematch with Forrest as Buffy runs off to find Adam sitting at his system of closed circuit monitors. Buffy manages to break off Adam's trademark bone skewer, but to her surprise, his left arm mutates into a gattling gun and he opens fire in the small room. As Buffy dives behind one of the consoles, Willow, Xander and Giles complete the spell, and their powers rush into Buffy's body.
Adam destroys the console with a single mortar shot, but Buffy rises from the rubble with magical, yellow eyes, speaking in Sumerian. Adam sends a long burst of machine-gun fire at Buffy, but the bullets are stopped by an invisible force field just inches from her. Back in the other room, Riley and Forrest are engaged in a fierce battle. Forrest throws Riley into a stack of Hydrogen tanks, causing them to leak. Riley picks one up and pushes Forrest back with it. Forrest grabs the tank and raises it over his head near the broken power line to hit Riley, who ducks behind one of the operating tables. As he swings forward, the hydrogen gas ignites, and Forrest is blown into tiny chunks of burning flesh. Back in the other room, Buffy uses the combined powers of Willow, Giles and Xander to ward off Adam's mortar attack. Buffy collapses Adam's weaponry telepathically, then in a blistering display of power, forces Adam against a wall, pierces Adam's chest with her hand, and pulls his Uranium power supply from his chest. Adam is no more. As Riley looks on, Buffy levitates Adam's power supply from her hand, and dissolves it into thin air.
With their work done, the spell wears off and all Buffy, Willow, Xander and Giles collapse with fatigue. A demon crashes through the barricaded door and almost gets to Willow, Xander and Giles, but Spike comes up from behind and snaps its neck. Giles scolds Spike for helping Adam with his plan but fatigue and the fact that Spike just saved their lives prevents him from doing anything about it. Buffy and Riley emerge from the secret lab, and the whole team goes to work securing the compound. Meanwhile, in a secret government conference room, the same powerful Government official who had spoken with the now deceased Colonel MacNamara proclaims the Initiative a failed experiment to harness the powers of the otherworld, and orders it burnt to the ground.