Cole is vanquished, but his child still grows in Phoebe's womb. The episode begins with Phoebe's nightmare of giving birth to a normal-looking baby boy -- and then watching helplessly as the Seer carries him away. The next morning, Phoebe wakes up exhausted. She tells Piper, Paige and Leo that she thinks the Seer is after her baby. Later, she apologizes to Paige for not believing her about Cole turning evil again. Phoebe is having hot flashes, not a typical symptom of pregnancy, and Piper persuades her to see her OB/GYN, Dr. Harris.
Dane, Cole's former top lieutenant, is preparing to be crowned as the next Source, but the Seer interrupts the ceremony, saying that she had a vision of Phoebe's baby as the new Source--and with her help, he'll be able to rule immediately. The dark priest doesn't agree at first, believing that a baby cannot lead the Underworld. The Seer, however, asks for a chance to prove her vision. The dark priest points out that Dane has no ties to the Source, and gives the Seer until tonight to bring them the baby.
Phoebe's hormone levels are unusually high for a mother in her eighth week--most likely due to the Seer's tonic. Dr. Harris wants to do a sonogram. Suddenly, flames shoot out of Phoebe's head. Piper is concerned, but the ultrasound looks normal at first. Without warning, electricity shoots through the sonogram tool and shocks the doctor. The doctor is okay, but Piper is concerned enough to cut the appointment short and take Phoebe home.
Back at the manor, Paige has found the Seer in the Book of Shadows. She is an upper-level demon who has served multiple Sources and is immune to most spells and charms. However, they can vanquish her with a potion made from her flesh. Phoebe remembers that her prenatal tonic contained some of the Seer's blood. Cole kept some extra bottles at their penthouse apartment. Suddenly, Phoebe yells "Bitch!" at Paige, and under the baby's influence throws her out of the attic window. Paige almost lands on Darryl but orbs away at the last moment.
Darryl is at the manor to help the sisters cover their tracks, since they're the only ones who know Cole is dead. He needs them to get his things and make it look like he abandoned Phoebe, then have Phoebe file a missing-persons report. They find the apartment still a shambles, forcing Paige to remove the evidence with a spell. The baby suddenly makes Phoebe knock Paige to the floor, further worrying Piper and Paige. Paige remembers Phoebe telling her the tonic was kept in a safe hidden behind a painting. They find the safe, and Paige orbs the door off its hinges. The safe is empty, except for a letter Cole wrote to Phoebe.
Phoebe is holding a bear Cole gave her when she found out she was pregnant. She opens her old closet--but it turns out to be a portal to the Underworld. The Seer reaches in and tries to draw Phoebe into the Underworld but the sisters and Darryl pull her back. Phoebe manages to pull off part of the Seer's earlobe for the vanquishing potion.
Back at the manor, Piper tries to give Phoebe some fruit since she hasn't eaten all day. Phoebe picks up a slice of watermelon, and it turns into a piece of raw meat revealing the baby preference. Paige completes the potion but the baby, through Phoebe, throws fire at her and the potion spills. This makes Piper declares to not have them be in the same room. Piper asked if there is enough earlobe that they can make another batch and sent Paige to do another again.
The Seer makes an offer to an imprisoned demon, the Tall Man, offering him his freedom in return for capturing Phoebe and bringing her to the Underworld.
Phoebe and Darryl meet with Inspector Miles from the missing-persons unit to report Cole's "disappearance." The baby stirs up more magic; apparently he doesn't like anyone badmouthing Cole. Phoebe has a sudden pain in her belly, and Leo can't heal her. They head back to the manor.
Piper finds out from Dr. Harris that there's considerable scarring in her womb, and it will be very difficult for her to ever have a baby. She takes it very hard, remembering she saw her future daughter. Phoebe and Leo rush into the manor; Phoebe is still holding her stomach. Flames shoot from the top of her head. Suddenly, the Tall Man teleports in. Piper tries to blast him, but it has no effect. Leo tries to hit him with a chair, but he absorbs the whole chair. Paige runs in to help. The baby forces Phoebe to kick Paige into the Tall Man, and they both disappear.
Piper and Phoebe find the Tall Man in the Book. There's no good information on the demon because he had been imprisoned for many centuries. Phoebe is distraught over what the baby is making her do. Piper gives Phoebe a glass of iced tea, but Phoebe suddenly throws it across the room. The "tea" turned out to be a potion to bind the baby's powers. Phoebe fears the baby is trying to take complete control of her.
The Seer sends Phoebe a vision of her killing Paige. The Tall Man returns, demanding that Phoebe come to him. Phoebe wants to go rescue Paige. Leo tries to stop her, thinking it's a trap, but Phoebe throws him out of the way--and it isn't the baby this time. Piper grabs the vanquishing potion and offers to go along. She grabs the vanquishing potion, but Phoebe shoots a beam of light out of her hand, which knocks both the Tall Man and Piper to the ground and shatters the potion. Phoebe then shoots another beam and vanquishes the Tall Man. Piper and Leo are horrified; the Tall Man was thought to be unvanquishable. Suddenly, Phoebe's eyes turn black, and she flames to the Underworld.
The Seer has been waiting for Phoebe. Despite Paige's pleas to snap out of it, Phoebe follows the Seer to a circle of candles as if in a trance. The Seer casts a spell to transfer Phoebe's baby to her own womb. Phoebe snaps back to herself, and the Seer tells her that the baby was never really hers--but she was the one who magically conceived it.
The Seer now claims the right to be the new Source, and brings with her Phoebe and Paige as human sacrifices for the ceremony. Dane strongly objects, and the Seer throws fire at him, vanquishing him. Phoebe realizes that magic cannot get out of their cage but it can get in. She and Paige summon Piper with the lost-witch spell.
The Seer takes the oath to become the new Source. She notices Piper in the cage, and is about to kill them when flames shoot out of her head. Phoebe figures the baby's power is too much for the Seer as well, and suggests making her tap into all of his power. The sisters start chanting the Power of Three Spell while the Seer tries to destroy them. However, her blasts bounce away. The sisters keep chanting, forcing the Seer to tap into more and more of the baby's power until it shoots out in all directions, killing every demon in the room. Finally, the Seer is overloaded by the baby's power and explodes, vanquished along with the baby. Vanquishing the Seer breaks the magic of the cage and Piper is able to kick down the door, freeing them. They take the Grimoire back to the manor, and Leo hides it under a mountain of rocks in the Andes so no more Sources can be crowned. Paige asks if they truly vanquished the Source. Leo replies that the Elders are celebrating in the Heavens.
Piper tells Leo about the scarring in her womb, but Piper told Leo she is still determined to keep trying. Piper gives Phoebe Cole's letter; it says that his love for her is all that's keeping him alive.
At the end of the episode, Phoebe hears Cole's voice on the wind, begging for her help.