Cole and Phoebe now rule the Underworld from Cole's apartment as the Source and Queen of all Evil. A meeting of high-level demons is in progress and Phoebe can't sleep with all the noise. Ironically, her reason for moving out of the manor was to find quiet. She wants some attention from Cole, but he's been in meetings almost constantly since his coronation. The Seer comes in with some tonic for Phoebe which is supposedly intended to strengthen her through the pregnancy. Phoebe doesn't understand why Piper, Paige and Leo haven't accepted her decision to be with Cole, but the Seer tells her that it's not in the nature of Good to compromise. Phoebe walks in on the meeting to call Cole to bed. She vanquishes two demons with her new flamethrowing power and the others shimmer away.
Paige is looking through the Book of Shadows for some way to get Phoebe back, but Piper doesn't think there is a magical way out since Phoebe chose to be with Cole. They've made several attempts to sway Phoebe back to good, with no success. Piper thinks Phoebe might attack them, so she makes potions just in case. Leo orbs in; he has word Phoebe is killing demons.
Cole is holding a meeting at his apartment with his top lieutenant, Dane, and several other high-level demons. They are making plans to kill several innocents. Phoebe walks in, and jokingly waves her hand as if to fry one of them. She kisses Cole and heads out. Cole follows her out. He isn't happy with her habit of vanquishing demons; it's making it harder to accept that their Queen is a (former) Charmed One. Phoebe promises not to vanquish any more demons, and even goes as far to personally apologize to them. However, in the process, she touches one and sees one of the innocents they've targeted, Greg Conroy, killed by that demon. She pours the tonic into a potted plant and heads out. The plant starts to rot away.
After Phoebe hears that the demon, Malick, is indeed after Greg, she flames over to the manor. Piper throws a potion at her, but Phoebe disintegrates it with fire. Piper isn't interested in talking unless Phoebe is ready to leave Cole, but Paige and Leo want to let her talk. Phoebe mentions her premonition. Piper thinks this may be a trap, but Paige and Leo think this may be their only chance to sway Phoebe back to good.
Piper, Paige and Leo orb to an alley Phoebe saw in her premonition; Phoebe flames in ahead of them. Greg walks around the corner. Malick shimmers in behind him, but Piper freezes the scene. She raises her hands to blast Malick, but Phoebe nudges her and knocks the blast away from him onto Greg's bike. Phoebe walks up to Malick, who kneels before her. To the dismay of her sisters and Leo, Phoebe merely orders him to leave. Phoebe doesn't want to kill demons anymore, but admits she missed her sisters and Leo. Piper tells Phoebe that her baby is corrupting her, and that they don't want her working with them as long as she's married to Cole. Leo tells her she must choose between good and evil--even if it means walking away from Cole. Phoebe flames away. Piper can't handle it anymore and walks away in disgust. She unfreezes Greg, who notices his missing bike. He goes back inside. Paige and Leo follow him.
Malick tells Cole that the Charmed Ones interfered with his attack on Greg--and Phoebe was with them. Cole, suspecting him of disloyalty, vanquishes him. At Dane's suggestion, Cole summons another demon, Raim, and sends him after Greg.
Paige and Leo are keeping an eye on Greg at an AA meeting he's attending with some of the juvenile offenders with whom he works. They're worried about Piper; they still remember how crushed she was after Prue's death. Paige tells Leo to go talk to Piper while she watches Greg.
Phoebe is continuing her advice column in spite of being Queen of the Underworld. However, her evil side creeps into her work; she is now suggesting such things as beating one's cheating husband with an office stapler. Elise is not happy. Phoebe is about to throw fire at her when Cole arrives. He lectures Phoebe over her having saved Greg, and warns her that he may face a coup if it appears they're playing both sides. Phoebe is contrite. Cole understands how Phoebe is struggling with dueling good and evil natures; he went through the same thing as Belthazor. However, he tells her she has to make a choice, even if it means walking away from her sisters. They flame away.
Leo finds Piper at P3 after closing time, drinking a bottle of whiskey. She feels responsible for Phoebe becoming the new Queen of the Underworld, and is kicking herself for not listening to Paige's warnings that Cole had turned evil again. She believes that since she is the oldest sister now, she inherited Prue's old job of protecting the family--and letting Cole "destroy" Phoebe is proof she's a failure. Leo admits he didn't see the signs either and tries to buck Piper up, but Piper freezes him. She takes another sip and falls down from the chair.
Paige follows Greg out of the meeting just as Raim shimmers in. He throws a light dart at Greg, but Paige knocks Greg out of the way. The demon throws another light dart and hits Greg on the shoulder. Raim is about to finish Greg off with an athame, but Paige orbs it out of his hand and throws it back at him, vanquishing him. Paige orbs to P3 to find Piper passed out (fell asleep drunk) and Leo frozen. While Leo heals Greg, Paige revives Piper.
The Seer walks in with more tonic for Phoebe, but Phoebe notices the plant in her room is completely dead. The Seer admits the tonic was not only meant to strengthen the baby, but destroy Phoebe's good side and turn her completely evil.
In the Underworld, a council of demons led by Dane summons Cole to the underworld. They have heard that Phoebe saved Greg. Cole assures them that the Power of Three no longer functions, and Phoebe's behavior is simply the result of hormonal fits from her pregnancy. Dane suggests that Cole take out Greg himself, "for morale". Paige is helping Piper recover from her hangover. Paige still thinks Phoebe can be saved, but Piper thinks she loves Cole too much to vanquish him. Just then, Phoebe walks into the manor and offers to help vanquish Cole; she knows that Cole is after Greg personally. She suggests using Greg as bait, with Leo orbing him away at the last moment. When Leo orbs in with Greg, "Phoebe" morphs into Cole and kills him with a fireball.
Cole flames back to his apartment to find Phoebe writing a goodbye letter to him. She tells him she's written a goodbye letter to her sisters as well, but doesn't know which one to send. Cole admits ordering the Seer to brew up the tonic; he wanted to spare her the pain he'd endured for a year and a half. Phoebe is upset, but still can't bring herself to choose between Cole and her sisters. Cole warns her that if he's overthrown, his successor will almost certainly kill Piper and Paige. Cole offers Phoebe a glass of the tonic, and Phoebe drinks. Thinking that Phoebe has chosen to be with him, Cole admits to having killed Greg. Phoebe runs into the bathroom and throws up the tonic.
Leo, Piper and Paige orb into the apartment. Piper blows Cole up, and while his body's molecules try to come back together, Paige starts to set up a crystal cage around him. Cole's body reconstitutes and he throws Paige against the wall, which sends the last crystal in another direction. While Leo heals Paige, Piper blows Cole up again and calls Phoebe for help. In the bathroom, Phoebe quietly begs Cole's forgiveness and comes out of the bathroom just as Cole's body reconstitutes. Cole raises a fireball and is about to throw it at Piper, Paige and Leo. Phoebe picks up the crystal. Cole tells Phoebe that killing her sisters and Leo is "for the best." The two kiss, and Phoebe places the last crystal in the circle, activating the cage. As Phoebe collapses into Piper and Paige's arms, Piper starts the vanquishing spell Phoebe wrote. Phoebe continues through Cole still saying he still loves her and always will. Phoebe helps finish the spell, crying through most of it, and Cole is vanquished. Phoebe breaks down in the middle of the room.
The next day, Phoebe is lying in her room at the manor, still crying over Cole. Piper and Paige come up to comfort her.