The second season of Nip/Tuck premiered on June 22, 2004 and concluded on October 5, 2004. It consisted of 16 episodes.
Sean has just turned 40, and he is already noticing it. His body is aging, and he has developed "the yips", making his performance during surgeries decline. Julia breaks the news to Sean that her mother, Erica, is coming to visit. Erica tells them that she wants a facelift - and she wants Sean to do it. Sean would prefer that Christian do it instead. Meanwhile, Christian is having problems with picky Gina, who is trying to keep Christian away from baby Wilbur, because it isn't his baby. Having his own problems with age, he is rejected by a 25-year old at a bar. Christian decides to hire a nanny, who he ends up having sex with, and later learns that she is giving the baby drugs to keep it from crying. Christian tries to convince Sean to have botox, but he refuses (at first). They perform surgery on a woman who was shot in the face nine months earlier. She is brought along by her gay friend. The two are having problems because the woman loves Chad, but Chad doesn't love her in that way, because he's in love with his boyfriend. We learn that Chad and the woman were planning on shooting each other, but she couldn't pull the trigger, so Chad was left unharmed. During Erica's facelift, Sean panics and can't do it. Christian is having some trouble too - he's slept with Erica, the night of Sean and Julia's wedding. The surgery continues. Later that day, Christian is having problems with Wilbur, so he calls Julia to come help him. She gets upset on how Christian can't handle his own responsibilities, and snaps at him for sleeping with her mother.
Sex gone wrong causes Christian to break his nose, but Christian is worried that Sean's medical condition will keep him from performing the corrective surgery. He consults a rival (female) plastic surgeon across town. Christian and Gina have sex, but she gets upset when Christian tells her that he's imagining the female plastic surgeon instead of her. Gina tells him that he looks hideous, so Christian decides to operate on his nose himself, which goes terribly wrong. Christian, trying to show that the McNamara-Troy partnership is worth something, tells Sean that he wants him to fix his nose. When Sean panics, Christian decides to go through the surgery without anesthesia, so they can do it together. Sean performs the surgery successfully. Meanwhile, Matt learns that Harry has been arrested for raping Cara Fitzgerald, and that Harry has told the authorities about the hit-and-run, and that Matt was involved. While under oath, Matt says that he had no involvement with the car accident.
Manya has had a "female circumcision" as a young child, so she wants to have corrective surgery. A man requests hair implants all over the exterior of his body. Sean meets Ava, a life-coach, and enlists her to help out Julia. In addition, Sean has problems with Erica, still staying at the house, and Christian has problems with Gina.
As Julia and Sean's daughter Annie faces puberty, they must both face the harsh realization of maturity and deal with their own issues about getting older. When Gina tells Christian he can no longer be involved in Wilbur's life, Christian is forced to reach out to an old flame in order to build a case to gain sole custody of Wilbur.
After a car accident due to cell phone use, Sean winds up in the hospital. As a result of the accident, Sean develops a phobia of driving and other dangerous things, causing a dent in his career. He thanks the car company because their safety features saved his life. The car company, wanting a point of view from this doctor who has been in a car accident, offers Sean a new car if he agrees to inspect the cadavers they use as crash test dummies after crash tests. Sean tries to take more risks, causing Julia to become upset. Trying to take more risks, Sean decides to go shark diving, and drags Matt along with him. After realizing how much he cares for his son, Sean decides not to follow through. Christian is reminded that his son is no longer in his life, and he turns for comfort in Julia, who reveals to him that Wilber is not his only son.
Bobbi Broderick comes to McNamara/Troy to have lipo so she could get a job at Saks. During the consult, she doesn't bother to read the contract she signs. After the lipo doesn't turn out to standards, she tries to get revenge against the firm by showing everyone how it "ruined her life" by showing up in restaurants and the lobby of the firm itself. Julia asks Ava to help Matt with his grades, and Ava eventually offers Matt sex in order to focus more on his schooling. Julia tries to speak with Ava about a trouble from her past - a huge mistake she made in college - and Ava realizes it involves Matt's paternity. A woman whose lips were burnt off goes in for a consult, and learns that the doctors would have to take skin from her vagina to fix her lips. She decides to do it, because her husband has never been intimate with her down there. Sean feels uncomfortable about the woman lying to her husband where the skin has come from. She tells her husband it has come from the back of her legs. Meanwhile, as Matt becomes more attracted to Ava, he is arrested after being caught masturbating outside her window. He seeks Christian to bail him out because he thought he could trust him, but Christian becomes upset for his ignorance. Matt lashes back by saying that he already has a father, and he doesn't need another one. After Ava and Matt finally have sex, the next morning Matt learns Ava has a son named Adrian - and they're the same age.
When local model Naomi Gaines is raped & disfigured by an attacker named "The Carver", Sean decides to repair her injuries on a pro-bono basis, thrusting McNamara/Troy into the local media spotlight, trying to overcome the slander caused by Bobbie Broderick. After getting caught sneaking into the house late at night, Matt lies by telling his parents he was studying with Ava's son Adrian. Adrian is forced to play along with the subject when Julia invites them all to dinner. Adrian reveals Matt & Ava's relationship, causing Julia to lash out at Ava & Matt. When Matt becomes uncomfortable with his increasingly demanding relationship with Ava, she reveals to him the secret that his mother is keeping from him.
A patient named Agatha Ripp comes in to McNamara/Troy. She reveals to Sean & Christian that she had a stigmata, but she says that it was a lie she said to the church so they would accept her, and that she really cut herself. People of the town turn to Agatha for blessing and renewed faith, despite claiming to be a fraud. When a "stigmata" appears on her legs, the doctors do a blood test to learn that it is not her blood. Meanwhile, Julia is experiencing shingles, which Sean attributes to guilt or pressure, and associates it with the Matt-Ava relationship. She breaks the news to Sean that the reason she is under so much stress - he is not Matt's father. Sean goes insane and aggressively hurts Julia. He rampages into the office where he beats Christian to the ground. He turns to the church, where he meets Agatha. She reveals everything was fake, and that a sister from the church snuck in and punctured her, and left her own blood so the church would not cut her program. Meanwhile, Liz reveals she is pregnant, but shuts Christian out, who wants to care for the baby. She experiences bruising and spotting, causing her to worry about 'the unknown'. Despite being impacted by Agatha, Liz has an abortion without telling Christian, who is upset that she got rid of the baby because she felt it would be handicapped.
Sean and Christian face the challenge of separating conjoined twins. The challenge is more complicated when Sean has difficulties working with Christian after learning the truth about Matt. Their constant bickering has been causing them to lose clients.
A man visits with Sean and Christian in order to be given breasts because of the fact his wife lost a breast to cancer. They refuse the job at first, but Liz talks them into doing it. After a while, his wife is overwhelmed with them, and the man wants them taken out, which eventually happens. The wife seems to enjoy them too much, which causes her to question her sexuality. Kimber has turned to the porn business after impatience caused her to turn back on her acting aspirations. A Real Doll (used for sexual purposes) of Kimber has been made, but Kimber thinks the vagina is too generic, and wants the doctors to fix the doll. Christian blasts the job and tells Sean that it's a bad idea, but Sean wants to follow through because Kimber offered a lot of money, and the practice lost money when Sean and Christian were on the verge of splitting. When Sean takes the doll home to work on it, he gets lost in the moment and has full sex with the doll, which has suction features in the openings to give a full orgasm. Sean realizes how sad he is, but then Kimber shows up to unexpectedly pick up the doll, and ends up having sex with the real Kimber. Julia has moved into an apartment, and wants to pick up some items from the house to furnish the kitchen, and she also asks Sean if she can spend the weekend with Annie. Sean lets her, despite the fact that he is angry throughout the entire conversation. When Julia shows up the next morning to pick up the waffle iron, she runs into Kimber, who is going to make Sean coffee after their night together. Upset, Julia makes herself over and goes to a bar, where she meets a man she likes. She gets drunk, and winds up in his room where he wants her to use a sex toy on him. She refuses, but then man tries to force her to do it. She makes her way to the bathroom, where she finds a phone and calls Sean, hoping that he will come and get her. She tries to make up with him, but all he does is give her money for a cab and leaves.
Natasha Charles, a blind woman, comes into have work on her eyes so she won't appear blind. Christian begins to fall for her, and he learns a great deal about beauty from her. In an attempt to get Sean back, Julia goes to a female plastic surgeon to have breast implants. Erica visits Julia in her new apartment, and has become upset with her new lifestyle. Erica talks to Sean, and he gets mad at her also. Natasha goes out on a blind date (no pun intended) with another blind person. Christian, at the same restaurant, tells him that she is not pretty like the man had hoped, and he leaves. Christian joins Natasha, and they go home together for an intimate night.
After Julia's accident in the previous episode, Julia turns to Sean and Christian to fix her face. Sean resists at first, but eventually decides to do it after Christian lies to him and says the woman that was going to fix her face botched several jobs. Sean tells Julia that he keeps trying to forgive her and wants to try to love her again, but that it wouldn't happen right away. Julia has an adverse reaction to the anesthesia and dreams during her surgery. Ava shows up in her dream as a different form of life coach, and guides her through this surreal life. Julia is married to Christian, which seems happy on the outside, but is really falling apart on the inside. They run the Troy/Troy partnership firm. When Christian decides to leave the practice, Julia interviews another doctor - Sean, someone she knew from high school. Trying to catch up on old times, Sean invites Julia and Christian to dinner. They meet his wife, Megan O'Hara, and their son Matt, who is on the nerdy side and has a bug collection. Megan is three months pregnant with a girl they plan on calling Annie, named after his grandmother. Julia is upset after a visit to Liz, an OB/GYN in this world, who has two kids. Julia cannot have kids with Christian, who wanted to have a biological child since he was adopted. Kimber, Julia and Christian's three-way partner becomes pregnant, and Christian refuses to get rid of it. We are revisited by several characters, including Mrs. Grubman, Jude, and Julia's friend Suzanne. When Julia wakes up in recovery, Sean is there waiting for her. She has realized that things would never work out with Christian, and that Sean was always the one she loved.
Maids and servants of a wealthy woman have a party while she is out of town, and they hire a cheap plastic surgeon to give them all Botox -- Merrill Bobolit. The women all have adverse reactions to it, and one of them comes in to have it fixed because bulges have formed on her forehead. Bobolit has now partnered with Madam Rose, who owns a chain of beauty salons. He performs unsanitary plastic surgery for lower prices in her basement, and they proudly promote this new invented "Bobotox". Christian tries to talk some sense into him, and eventually learns that Merrill is hooked on the anesthesia, and is constantly high on it - even during surgery. Christian acts as his sponsor in an AA-type rehabilitation group. Merrill becomes furious with Christian after a girl he wanted flirts with Christian. Meanwhile, Matt gets upset at Adrian for wearing his leather coat to school while soliciting drugs to other students. After Adrian refuses to give him the coat back, they get into a fist fight. Since the coat belongs to Matt, the drugs in the pocket are pinned on him. Christian is called in instead of Sean along with Ava, and Ava comes up with the idea to bribe the principal, Ms. Wentworth, with pro bono plastic surgery. After getting off free because of the surgery, Adrian and Matt decide to be friends. While having a conversation in the bathroom at school, Adrian urinates in one of the soap dispensers, and both Matt and Adrian get called to the principal's office again. Sean comes in this time along with Ava, and he forces the truth out of Adrian and Matt, and snaps at Ava. Sean punishes Matt by sentencing him to spending his afternoons at the office doing handiwork and cleaning. Matt realizes he likes spending time there. Adrian has had the last straw with Ava's harsh treatment, and they share a meaningful moment as mother and son, but it turns weird when they begin to make out.
Sean and Christian repair the face of a woman abused by her husband; Sean and Julia confront Ava about her relationship with her son Adrian.
Beauty is a curse on the world. It keeps us from seeing who the real monsters are. Another victim of the Carver shows up to have his face fixed - this time it is a male, who was both raped and carved. They agree to fix him. A local news station does an interview with Sean about the pro bono work on Carver victims. The Carver finds his way into Sean's home. After Sean gets out of the shower, the Carver drugs him up and has a conversation with him. He slices his right cheek, and tells him that if he fixes another one of his "masterpieces", he is going to kill him. Julia helps him recover, and Sean tries to win her back - but she reminds him that she is happy with Kevin. Meanwhile, Gina tells Christian that she is HIV positive, meaning that Christian may be also. He calls his past lovers, including Manya, Erica, and Grace. He visits Kimber on the set of a porn movie, which she is directing. She tells him that she got tested quite recently because she's in the business, and that she's clean, which slightly relieves Christian. He has one more call to make - James and Wilbur (now known as Gabriel). They both come to visit, and Christian becomes very emotional. Christian's tests come back negative, and he visits Gina in the hospital with the good news. He lies down next to her in her hospital bed after a heartwarming conversation, and they fall asleep together.
Joan Rivers consults with Sean and Christian to have all of her plastic surgeries undone, because she wants her grandson Cooper to learn that you don't have to be perfect. When she ultimately learns what she will turn out like after the work has been finished, she decides to give up on her original plan and asks the doctors to schedule her for a facelift the next morning. Matt is concerned about Ava, who seems obviously depressed. He suggests they go away to Paris and start a new life together, which she reluctantly accepts after some convincing. Matt goes to McNamara-Troy to steal drugs for her to take with them. Christian finds him, and gets upset when he learns Matt is going to Paris. Christian goes to have a talk with Ava, and when trying to make a point using sex, he learns that Ava is really a transsexual. Julia, Sean, and Christian spend the night researching, and trace their way to Maryland and a Gender Reassignment center. They learn that Ava's surgeon was a retired doctor by the name of Barrett Moore. Avery was a homosexual admirer of his, but Barrett could not love him the way Avery wanted him to. He perfected his plan for surgery, and made Avery a woman. They married, but their marriage was not perfect. Since they could not conceive, Barrett used a surrogate, and Adrian was born. Ava could not live with the pain, so she left with Adrian when Barrett was not home. Julia confronts Ava, and tells her that she knows her secret - and that she will reveal it to Matt if she does not break up with him by the end of the week. Ava needs one more surgery before she's complete, and Sean and Christian call Barrett in to help. Barrett asks Ava if he could meet Adrian, and she agrees to let him do so. When Matt comes home with the plane tickets, Ava gets upset by his constant mess making, and breaks up with him. In tears, Adrian comes home with a knife hidden behind his back. He once again tries to get his problems spoken. She tells him that Matt is out of the picture, and that they're going to go away to Paris together to start over. Adrian still knows something is missing, and we hear the noise of a stabbing. Adrian killed himself. He never got to meet his father. Upset, Ava decides to leave for Paris alone. The entire family - Sean, Julia, Annie, Matt, and Christian - have dinner together, very similar to the previous season finale. Sean repairs another victim of the Carver. Escobar lives in Sean's head as his conscious and tells him how to face the demon down. Sean decides he needs to lure the Carver to his house, and face him man to man. He has security cameras set up for protection, and brings a gun to bed with him. As the Carver creeps through the dark hallways, the Carver strikes. Sean is alone in his bedroom, and Christian has been slashed by the Carver.