Tess dreams of her childhood, when she was a young girl at an orphanage, listening to her music box at night in the ward where she's locked in. Once she is sure her guards have left, Young Tess removes a makeshift key from a floor panel where it's hidden and opens the door. She runs to the front door but discovers it's locked. She finally takes refuge in a cupboard, but a woman pulls her out and drags her away, leaving the music box behind.
Tess wakes up from her dream and hears the same music. She goes to the study and finds the music box waiting for her.
Lois is unpacking a box when Clark comes in. He notes that she's reluctant to admit that she moved in, and Lois explains that the box contains her mother's keepsakes, and her father sent her to them. Her mother, Ella, gave them to Lois after she found she had cancer. Lois explains that she never visited her mother during the five weeks she was in the hospital, and never said goodbye to her. There are several video tapes in the box, and Lois takes the first one out. She wonders if she can face it, and Clark assures her she shouldn't feel guilty for refusing to open up old wounds. Lois wonders if he has something missing in his life since the Jor-El construct abandoned him, but Clark insists that it's different. She insists that Jor-El cared for Clark, but he avoids the question and leaves for patrol. He offers to stay if she needs her, but Lois says that it's okay. Once he leaves, Lois contemplates the videotape.
Clark arrives at Watchtower in response to Tess' call for help and finds her going through old photo albums. She explains that someone broke into the mansion, and left her the music box, which has a tag saying, "Happy Birthday, Tess." Tess describes her nightmare and where she found the music box. There are no pictures of it in Tess' photo album. Clark finds an older tag beneath the birthday tag, with the faded words "St. Louise's Orphanage" on it. Tess doesn't recognize the name, and Clark identifies it as an orphanage belonging to an elderly benefactor nicknamed "Granny Goodness."
In a basement room, Granny tells a young girl that her memories are holding her back, and that once she's done, the girl will thank her. She then begins to draw the memories out of the girl's head as the child screams in terror.
Lois watches her mother's first tape. On it, Ella explains that she asked the Colonel not to bring the girls so that they would have happy memories of her. She asks Lois to play the tapes and think of her, and then says not to let the loss of a parent interfere with her chance to find happiness with someone in the future. Ella assures her daughter that she will always love her.
Clark and Tess go to St. Louise's Orphanage after finding a photo of Tess standing on the doorstep. They claim to be doing a story on the orphanage, and Granny Goodness is eager to have them there. As she has the girls sing, Clark hears a girl crying with his powers and superspeeds away to investigate. He finds the girl strapped to the chair, and she explains that her parents just died in a car crash, and Granny was going to wipe her memories. Clark frees her and starts to get her out, but hears the sound of metal on metal down the hallway. He hides the girl in a room and goes to investigate, and finds women sparring with each other using battle weaponry. As he enters the room, he discovers that they have a forge of kryptonite flames. Weakened, he is easy prey to their attacks and one of the women, Harriet, informs him that he's the only one who needs saving.
Granny brings Tess into the house and says that she knows that Tess is an abandoned soul. She talks of how some of the older ones never find a home, and that she's been training them to conquer society. Granny shows Tess a gallery of her graduates, and Tess sees the cupboard from her childhood. She finds the scratch marks that she left on the side, clutching desperately as she was dragged away, and Granny says that she sent the music box to draw Tess back. She reveals that one of the gallery photos is of Tess.
At the farm, Lois reads the Kryptonian journal when Shelby comes up. She explains that she's realized that Clark can't move forward until he deals with the void in his life left by Jor-El's absence. She notices a journal sketch of the teleportation disk and goes through Clark's drawers. She finds a drawing of the Kawatche caves and realizes the disk is the key. Searching behind a bookshelf, she finds the key where Clark has hidden it.
Tess asks why she has no photos of herself before the age of five, and Granny says that Tess' parents didn't have her then: Granny did. She insists that she could never hurt Tess, and was training her to realize her full potential. However, her birth parents found her a home and took her away, and they were too powerful for Granny to fight back. However, when Granny learned that Zod had all but killed Tess, she went to the hospital and transferred her to Cadmus Labs, where the scientists cured her. Granny assures Tess that was the strongest of her girls, and she's her true family. With Tess' power, they can accomplish great things together in the war that is to come. She says that her girls will take care of Clark. Tess goes to find him, but Granny gestures and telekinetically slams her away. Tess runs away and finally takes refuges in her old room. Granny seals the windows and tells her that none of her girls ever leave her, and she plans to keep Tess forever and force her to serve as a solider in the coming war.
In the basement chamber, the orphan warriors string Clark up. He tries to get through to them, but Harriet insists that no one could love them as much as Granny, who will never leave them. She starts to slice Clark open, saying that a great fury will consume the world, but Granny intervenes and sends the girls to their rooms. Clark insists he won't let Granny ruin any more lives, but she tells him that she will bury his memories so he can live without a painful past.
Tess uses the hidden key that she made 20 years ago to get free, and runs downstairs. Harriet intercepts her and the two women fight. Tess throws her through a window and kicks Harriet unconscious, but another orphan girl wielding a whip lashes out and chokes Tess.
Lois teleports to the Fortress and calls out to Jor-El, saying that she understands how he made a hard decision by trying to protect Clark. He calls on Jor-El to support his son and stop Clark from fulfilling his potential as a hero. When she gets no response, Lois angrily insists that Clark is more of a Kryptonian than Jor-El ever will be. An energy field sweeps Lois up into the air, immobilizing her.
Granny straps Clark into a chair and prepares to strip him of his memories, assuring him that he'll be much happier without the pain of being abandoned. As she prepares to drain his memories, Clark uses his superbreath to freeze the chain holding the ventilation hood above the kryptonite forge. It falls, cutting off the flames. Clark revives and frees himself, but Granny has slipped away. He goes upstairs and finds the orphan warrior choking Tess. Clark burns through the rope and subdues the girl in less than a second. Tess admits that she thought she could handle the situation on her own, but Clark says that he wasn't going to abandon a teammate.
Clark returns to the farm and realizes what Lois does. He goes to the Fortress and demands that Jor-El release her. He pulls Lois free and she calls upon Jor-El to come out. Clark is fine with Jor-El remaining silent, but Lois insists that he try to resolve matters with his father. An image appears: a projection of Jor-El and Lara, recorded in the last moments before the destruction of Krypton. They know that Clark bears elements of both of them within him, and assure Clark that he was born of a great love. They refuse to go with him, but promise that they will always love hm.
Granny meets with her two conspirators: Desaad and Godfrey. Desaad explains that Godfrey has been chosen by their dark lord to serve as a prophet, and Darkseid's third minion. Desaad binds people's bodies at his clubs, Godfrey breaks their spirits, and Granny clears their minds and prepares their minds for Lord Darkseid.
At the farm, Clark assures Lois that Ella is still watching over her, and he doesn't think Lois is crazy. She admits that her mother is the bravest person she knows, and Clark wonders if their parents could have handled saying goodbye to them. Lois assures him that there's a part of Jor-El that is very human, and Clark realizes his father carried the burden of Krypton's destruction. He thanks Lois for bringing him and his father together. Lois then shows Clark her toothbrush and says that she's agreed to move in. As Clark goes to get their coats for a night of karaoke, Lois finds a letter from her mother saying it's for her wedding day. As she goes out, Clark contemplates the engagement ring he has bought for the occasion.
At the manor, Tess reads the birth certificate she found at the orphanage and remembers the day that she was brought there... by her father, Lionel Luthor. The certificate shows that her mother was Pamela Jenkins, and that Tess' real name is Lutessa Lena Luthor. Realizing that she is Lex Luthor's half-sister, she goes to the window and wishes herself a happy birthday.