Old friends Sean (the family man) and Christian (the playboy) are partners in a plastic surgery office. Their relationship is under fire after Christian operates on a Colombian drug lord who pays him in drug money. Sean's family life is also in upheaval, and he is headed for a mid-life crisis.

Twin sisters want plastic surgery done to look different from each other. Sean moves out so he can experience life as a single man. Matt decides to try and perform a circumcision on himself after his girlfriend sees his penis. Christian is plagued with thoughts of Julia.

Sean and Julia discover Matt has tried to circumcise himself. The business is sued by a faithful client after Sean accidentally leaves a surgical tool inside of her body. Meanwhile, Christian and Grace struggle with a mentally unstable patient.

Matt accidentally hits Cara with Henry's car, and calls Sean in to help when Cara's mother, for religious reasons, refuses drugs and surgery to treat her injuries. Christian discovers that a patient used plastic surgery to hide a revolting crime and it brings up terrible memories of his own childhood.

Sean and Christian learn that they have to take a test in order to continue practicing. Sean and Megan visit a doctor to learn that there is nothing they can do for her. Mrs. Grubman returns to get an operation on her and her fiancé. Christian passes his test, but Sean walks out. Megan commits suicide. Julia finds out about Sean's affair with Megan.

Christian learns that Kimber and Merril are engaged. Escobar continues to have the surgeons do things for him. Liz is sent to Bermuda after being shot in the leg by one of Escobar's people. Sean goes to kill Escobar. Escobar makes a deal with Sean; a new face for their freedom. Christian learns, in the delivery room, that he is not the father of Gina's baby. Julia returns to get the paternity test she had done a while ago. The doctors do surgery on Escobar, and give him the face of a criminal even higher than Gallardo on the Most Wanted List - Armand Ortiz. Ortiz is arrested at the airport for bank robbing and killing a federal agent.

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.

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.

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.

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.

After Christian's Carver attack, Sean must look for a new partner to keep the practice going. Sean has to surgically separate an obese woman from a couch she has spent the past three years on. Julia realizes that she has to make a decision about the future of her marriage.

The Carver strikes at a sorority house. His identity is revealed. Ariel's dad kidnaps Matt and Cherry. Ariel's dad forces Matt to make a life threatening decision, while the carver tries desperately to get his last minute revenge. Julia discovers that there might be something wrong with her baby.

Sean and Christian may be celebrating a milestone surgery, but it looks like the future of McNamara/Troy is in jeopardy. Julia tells Sean some devastating news about the baby. Christian decides to redecorate his apartment after a disturbing appointment with his psychiatrist.

It's the year 2026. Conor is getting the whole family together. In the present, Julia and Sean's marriage is at a crossroads.

Sean considers selling his shares of the practice to Christian and Michelle, although Michelle's past starts to threaten her future with Christian. Meanwhile, Escobar's wife needs cosmetic surgery.

Sean and Christian have relocated their practice from Miami to Los Angeles. Being new to the city they find themselves having to start from scratch business wise. What they thought would naturally fall into place turns out to require some foot work. So Christian and Sean hit the town and begin discovering a whole new world.

Sean and Christian learn about the glamorous side of fame and the price that many are willing to pay for it. Julia visits Sean, Christian and Liz in Los Angeles with a surprise announcement.

After surviving the attack by Colleen, Sean's physical and emotional well-being are still feeling the effects. Meanwhile, Christian receives some disturbing news after lending Liz some moral support with her breast cancer scare.

Aidan Stone, a down-on-his- luck writer who has written a biopic about Sean, wants to use it to relaunch his career. Christian is asked by Kimber to give a Botox injection to her daughter so she has a better chance at becoming a baby model. Sean and Christian have been asked by a yoga instructor to perform a procedure in which neither have ever done before.

As Season 6 begins, Christian has news for Liz and the economic downturn has hit McNamara/Troy hard. But the boys might have found a lifesaver in Dr. Mike Hamoui (Mario Lopez), who's now in L.A. and has found a very profitable niche specialty. Meanwhile, Sean's relationship with Teddy Rowe (now played by Rose McGowan) has blossomed, and Matt, who's down on his luck, takes up mime.

Both Matt and Alexis Stone request unusual surgical procedures from Christian. Erica discovers the horrible truth about her new husband. After a lifetime of torment from her mother, Julia seeks revenge upon her.

When Sean and Christian win a prestigious award from their alma mater, Sean recalls their college years and endures past pains. A new patient who self-mutilates due to a genetic disorder comes to McNamara/Troy for reconstructive surgery.

Sean and Christian reflect on their relationship. They also remove a scar from an elderly Japanese man and have a surprise for Liz. Meanwhile, Christian makes a deal with Ava.