While Amelia and Owen's wedding continues, Andrew is brought to the ER after being assaulted by Alex, leading Meredith and the other doctors to the hospital to help. Meredith faces a dilemma about protecting Alex or telling Bailey the truth about the assault. Meanwhile, April and Catherine Avery clash about naming the new baby. Nathan and Meredith continue to work out their relationship at the same time as they try to hide it from Maggie, who is affected by Andrew's assault. In the end, Meredith tells Bailey the truth, but not before Alex turns himself in to the police.

Absent: Jessica Capshaw as Arizona Robbins due to maternity leave

On Andrew's first day back, Alex is charged with felony assault in the second degree. When he's distracted at work, a kid's newly transplanted kidney ends up jeopardized, causing Bailey to decide that Alex can no longer work as a surgeon and demote him to work at the Denny Duquette Memorial Clinic. April has trouble letting go of Harriet, who gets to go home with Jackson. Jackson asks April to move in with him so she can recover. Stephanie proves to be a good friend to Jo, who tells Alex she doesn't want to be with him after what he did. Per Meredith's request, Nathan turns Maggie down when she finally asks him out, but Maggie's not planning on giving up just yet.

Absent: Jessica Capshaw as Arizona Robbins due to maternity leave

A car crash at a funeral makes for a hectic day in the ER and Stephanie has to figure out what to do with the corpse. April can't help but come to the hospital when she gets bored taking care of Harriet. Meredith doesn't want to listen to Maggie talking about how asking out Nathan has ruined work for her, causing Amelia to mediate between the two. Arizona returns to Seattle after a visit to Callie in New York and finds herself caring for Andrew, but she also misses working with Alex, who's determined to keep working in the clinic so he can come back from what he's done. When Bailey's too busy, Ben teaches Tucker a lesson after he hit someone.

Alex has a terrible day in the Clinic when nurse Timir keeps bossing him around and won't allow him to go to his strategy session with his lawyer. He turns his day around by diagnosing a very rare condition, Ehlers-Danlos syndrome, thus saving the patient's life. April and Jackson are walking on eggshells with their current living arrangement, but they agree to keep living together after venting their frustrations. When their patient deteriorates, Meredith fears Nathan supported her decision because of what's going on between them and decides she wants to be just colleagues. Jo and Andrew bond since they can't talk to anyone else about what happened. Amelia and Owen come clean about horrible things from their pasts and decide to have children.

Bailey and Meredith find themselves pitted against one another when both of their patients are in need of a liver transplant. Bailey frets that when she asks her elderly patient if she'd give permission to redirect the liver to Meredith's 25-year-old patient, she'll oblige; however, to much of everyone's surprise, Bailey's patient denies, leaving Meredith's patient in dire need. Amelia thinks that she's pregnant and starts spreading the news to everyone except Owen. When she breaks the news to him, she takes her first pregnancy test which reveals she's not.

Having trained to become better at another hospital, Leah Murphy re-joins the staff of Grey Sloan to learn from Maggie. When he's at the court house to have a trial date set, Alex advises a pregnant woman to have her rash checked out at the clinic; she's found to have pancreatic cancer. Alex butts heads with Bailey so the patient will receive a surgery that means she won't have to terminate her pregnancy. Andrew appears to develop feelings for Jo. After dodging Owen all day, Amelia confesses to Alex that she's relieved she's not pregnant because of what happened in Los Angeles. Catherine decides it's time to investigate why so many past and present residents have needed second chances.

Miranda and Catherine hire an education consultant, Dr. Eliza Minnick, to overhaul the training at Grey Sloan. Maggie finds a notebook that belongs to Eliza; it contains a list of Attending's names and Maggie is at the very end - she says that she's never been at the end of any list. Amelia and Owen fight over which procedure to do first on a patient. Stephanie assists Amelia during the operation while Owen monitors the patient. April goes on a date with someone she found on Tinder and tells Jackson it went great. However, she later tells Jackson in the observation lounge that the date went bad. Maggie teaches Murphy on a high risk procedure while Eliza is present in the OR and Andrew is observing. Dr Minnick wants to teach Andrew a procedure so she nicks a vessel so that Andrew can stop the bleed and learn. Maggie admits she is not a good teacher, but she is a genius and a rockstar. Amelia tells Owen she does not want a baby. Arizona confronts Eliza about the list as to why her name was not on it. Eliza says that the list was only for learning peoples' names, and she would never forget Arizona Robbins.

A male patient is wheeled into the OR where Meredith, Owen, and Stephanie are waiting. Meredith has been up for 48 hours and Owen at least as long. Richard shows up to help having napped all day. Richard wants the patient to be given a name; he picks Gail, a cello player and music teacher. Each of the doctors has a flashback to a tragic incident from their past. Owen flashes back to working with his sister. She tells him to cut it out, meaning the liver, and he does. Stephanie is asked to contact UNOS to get the patient added to donor list. Stephanie determines the patient has an autoimmune disease, ITP. The doctors argue as to what needs to done at each stage in the OR. The patient is identified as Carl Henley from a photo they took of him to show a woman who called about her husband. Gail was Richard's mother, who had pancreatic cancer and died when he was ten. Meredith eventually suggests using part of Carl's own liver, calling it a hail Mary. The repaired liver is put back in, before moving him to the ICU. Meredith apologizes to Richard for the things she said.

Absent: Justin Chambers as Alex Karev, Chandra Wilson as Miranda Bailey, and Caterina Scorsone as Amelia Shepherd due to maternity leave.

A building collapse crowds the hospital with injured people. Looking for forgiveness, the landlord confides in Ben that he didn't have the money to fix the damage caused by an earthquake last year, leading to the collapse. Maggie and Richard's 12-year-old patient dies on the table. Having overheard Ben and Stephanie talking about the landlord, the girl's parents seek to avenge her death. Richard finds out that Eliza will take over his job and confronts Bailey about this. Maggie and Jackson gather the other attendings to stand up for Richard. Arizona and Eliza continue flirting in spite of the latter's arrogant side. Fearing the subpoena, Jo tells Alex about her violent marriage, making him reconsider taking the plea deal and going to jail for 2 years. While waiting for the DA, he listens to a voicemail Meredith left him after his goodbye to her. Meredith tells him he's stronger and bigger than giving up and promises him she'll go down swinging for him, making him doubt taking the plea deal. Amelia takes off and leaves Owen with a note, asking him not to blame himself for it.

On the day before Alex's trial, Bailey, Arizona and Jo drive with medical equipment including an advanced ultrasound machine to a maximum security women's prison hospital to treat a violent teenage inmate and her unborn baby. Jo bonds with the inmate, who says that she had good times with her mother in the past and that her mother will be taking care of the baby for her until she is released. However, her mother is downstairs and tells the doctors that her actual plan is to adopt the baby. The doctors wrestle with whether to tell the inmate about this news, given her violent tendencies. When the inmate goes into labor she demands to see her mother. Jo finally says that she is downstairs but refuses to come up, and the doctors help the inmate through the delivery. Later Arizona scornfully tells her mother that the delivery was a success, and asks whether she will abandon this baby too if she turns out bad. Meanwhile, Bailey learns about the realities of patient care in a prison environment. On the way back home, Bailey tells Jo that Alex plans to take the plea deal and will be going to jail, which makes her throw up.

Note: Only Chandra Wilson, Jessica Capshaw, and Camilla Luddington make physical appearances in this episode to accommodate various main cast members' maternity leaves. Ellen Pompeo provides a voice-over role only.

Maggie and Meredith find out that Alex's trial has been indefinitely postponed, leading them to think that Alex has taken the plea and is therefore in jail. Meredith sets out to find him, but to no avail. Owen is looking for Amelia, who's hiding at Stephanie's place. Owen finds out when Stephanie lets it slip that she asked Amelia to look at their patient's scan and he asks her to ask Amelia to come home, though Amelia refuses. Maggie, April, Nathan, and Jackson spend all day denying Eliza Minnick access to their OR whereas Richard allows her to join him so he can demonstrate that he's ready to fight her, leading to Bailey confronting Richard and revealing she's not the only one who felt this change was needed. Arizona and Leah work on a pregnant mother who was in a car accident caused by her husband. Allowing Leah to work on the baby while she's dealing with the mother, Arizona puts Eliza's method to work, which Eliza interprets as Arizona being on her team. Ben spends all day working alongside and covering for a grumpy Jo, who refuses to talk about what's happened with Alex. Andrew is surprised when Arizona admits that she misses Alex. After a long day, Meredith finally finds Alex in her bed, where he's been sleeping all day.

Alex reveals that Andrew made the D.A. drop the charges by threatening to otherwise tank the case with a (fake) testimony. When Alex confronts him about his reasons for doing so, Andrew states he did it because Jo's been through enough. Alex gets his job back while Meredith gets suspended for refusing to let Eliza into her OR. Jo, who spent the day at home, only finds out about Alex later and goes to visit him at Meredith's. Maggie's mother Diane comes to Seattle to have Jackson remove a rash, but it turns out she's suffering from inflammatory breast cancer. Jackson helps her prepare to tell Maggie, but before she can do so, Maggie has an outburst, revealing she's still struggling with her mother destroying her parents' marriage. Richard finds out that Catherine's on Bailey's side. Bailey hires April as Interim Head of General Surgery. Amelia continues to hide out at Stephanie's apartment, and Owen decides he's done waiting for her.

Dr. Minnick implements phase 2 of her teaching plan, where two residents a week get to lead a surgery from start to finish. Ben's first experience is ruined by Bailey and Webber arguing and Stephanie's 9-year-old patient dies. Stephanie is comforted by Webber, while instead of teaching her how to deal with loss, Eliza flees. Arizona learns that she's never lost a child before and comforts her. April steps in as interim Head of General Surgery but the attendings give her the cold shoulder, especially Maggie, who believes April deserted Webber and is now on Bailey's side. April and Maggie are forced to work together on a patient of Meredith's, who's reluctant to have a surgeon she doesn't know operate on her. Catherine bonds with April and takes her out to dinner to celebrate her new job.

Absent: Justin Chambers as Alex Karev and Caterina Scorsone as Amelia Shepherd due to maternity leave. Ellen Pompeo provides a voice-over role only due to maternity leave.

Alex returns to the hospital, but finds himself doing resident work because of Eliza's teaching method. Bailey visits a bored Meredith in an attempt to get her to agree to come back, but Meredith only does so when Webber drops by and convinces her not to do this to her career just because of him. April, Webber, Alex, and Jo get caught in a moral dilemma when a mother's only kidney dies in the middle of a kidney transplant to her son. A possible solution means accepting a kidney from the abusive husband whom the patient left, which hits close to home for Jo. Maggie and Nathan treat a patient with mental illness who disappeared on her parents 12 years ago. Arizona has to hide her new friendship with Eliza from her colleagues, and the two of them end up kissing.

Richard is revealed to be sleeping at the hospital, as politics within Grey Sloan Memorial boil over and spill in to his marriage with Catherine. Alex receives a tough peds case on a newborn baby with a heart problem. Tackling the case with Andrew, who is now "cool" with Alex, they together proceed to go through with a procedure until Nathan is brought into the case. As Alex and Nathan clash over different surgical procedures, each of them ask Andrew to contact different people as Andrew juggles whose orders to obey. April, Jackson, Webber, and Catherine are in the midst of a tough trauma case of a man who had an accident with another man and a deep fryer. As they begin their operation, Catherine tries to talk with Webber about their marriage and coming home which causes awkwardness within the OR. Meanwhile, Eliza invites Arizona out to a date at Arizona's house while Meredith hears about the growing conflict between Nathan and Alex and tells Nathan to back off on Alex's patient, causing Nathan to storm away in anger while it is revealed that Andrew called UNOS betraying Alex. As he prepares to go into his surgery, Alex sees that Andrew decided to obey Nathan which causes him to call Maggie who tells the two surgeons to get their act together. After his surgery, Webber accidentally walks in on Eliza and Arizona kissing, exposing their secret relationship. Meredith, who hears about the fight between Nathan and Alex, tells Nathan to back off and to not fight with Alex, causing Nathan to give her an ultimatum about their relationship, while Catherine and Richard's marriage lies more divided than ever before.

April and Jackson travel to Bozeman, Montana to perform a throat transplant on a girl, leaving Harriet with Catherine. The two discover they still need to get consent from the donor's heartbroken father, for which Jackson uses his experiences with fatherhood. However, when a lesion is discovered on the donor, the transplant is off the table, meaning a laryngectomy is the girl's only option despite her parents' objection. April discovers that Jackson took the case because his father owns a diner near the hospital, and encourages a distracted Jackson to go talk to his father so his head can be in the game for their patient. Jackson does so and discovers that his father left because being an Avery didn't fit him, and that he has a happy life and never actually missed his son. Jackson comes up with a solution for the girl and he and April pull it off. They end up sleeping together and agree that this was the reason Catherine had Meredith switched for April. Before returning to Seattle, Jackson goes to tell Robert that despite being glad to have met him, he's not actually his father.

Note: This is the first episode not to feature Meredith Grey since the pilot due to Ellen Pompeo's maternity leave. Only Jesse Williams and Sarah Drew appear in this episode as Jackson Avery and April Kepner respectively.

After receiving chemo at home, Maggie's mother returns to Seattle to undergo a mastectomy, performed by Jackson. Maggie can't understand her mother getting a breast augmentation, only to learn the devastating truth later. Stephanie meets one of her idols when the man's wife collapses during a hike. The woman has a brain bleed, but the surgery is very risky due to her comorbidities. Her eventual death has Stephanie questioning her profession, and Andrew admits to her that he loves Jo. After he tells her to figure out what she wants, Amelia tells Owen that she feels suffocated by him and that he doesn't get to set the rules in their marriage. Amelia questions if he's actually ready for parenthood, which may turn out quite differently from the dream he has. Meredith wants a reason to date Nathan. He talks about how he fell in love with her and how he feels about her, leading to her agreeing to have dinner with him. Arizona and Webber clear the air between them. A complication during Diane's surgery leaves Maggie devastated.

A spot on a scan alongside her chest wall causes a downward spiral for Maggie's mother. After surgery to remove the left-behind mass, Diane is found to have a metastasis in her liver. Meredith refuses to operate while Maggie thinks it's the way to go, resulting in Diane firing Meredith from her case. Bailey does the surgery when Maggie gets her hopes up about a trial, which Diane enrolls in after the successful surgery. Despite all the side effects, Diane has a good day and she teaches Maggie to cook lasagna, but she starts coughing up blood during a dinner with Maggie's friends. Richard fixes the esophageal tear in surgery, but Diane's health continues to deteriorate. Diane thinks Maggie will be hurt if she stops fighting, but Richard convinces her that Maggie's strong enough to handle it. Diane then stops the treatment and, after imparting wisdom and offering advice to her daughter, she passes away. Richard realizes he's not a father figure to Maggie and calls in Bill Pierce to comfort her. He also buries the feud with Bailey. Nathan and Meredith agree their timing's off and decide to postpone their promised dinner as Maggie would need Meredith to be there for her.

Absent: Camilla Luddington as Jo Wilson due to maternity leave. Jerrika Hinton as Stephanie Edwards. Giacomo Gianniotti as Andrew DeLuca.

Stephanie and Andrew have to take care of intern Isaac, who has abdominal pain and insists it's not "internitis" as Stephanie thinks. Maggie teams up with Arizona to remove a delicate tumor from a fetus's chest while her colleagues worry she's not ready yet, given it's her first day back. Meredith agrees to hang out with Nathan to see if it could go somewhere before she tells Maggie. When Nathan finds out about her and Eliza, Arizona befriends Nathan and gives him some well-intended advice about dating Meredith. Richard and Bailey begin to work things out between them while Jackson attempts to console a distraught Maggie.

Absent: Camilla Luddington as Jo Wilson due to maternity leave

Nathan and Meredith end up on a flight to a conference together. She tries to ignore his moves but ends up having sex with him in the bathroom, insisting it doesn't mean anything. After heavy turbulence hits, Meredith and Nathan tend to the injured while receiving help from Harrison Peters, a pediatric dentist. In a quiet moment, Meredith tells Nathan about her own plane crash and losing her sister Lexie. One of their patients starts showing signs of an epidural brain bleed while the pilot is unable to land the plane because it's caught between two storm systems. Meredith continuously has to relieve pressure on the man's brain with a needle and syringe on the shaky plane, while Nathan has to save a man with pulmonary hypertension. When the plane finally lands, Nathan questions how Meredith can still be scared of letting go of Derek and starting something with him. She then decides to ignore her fear of yet again losing someone she cares about, and agrees to give it a chance.

Note: Only main cast members Ellen Pompeo and Martin Henderson appear in this episode.

April, Andrew, Stephanie, and Richard have bad news for their patient and her new boyfriend when she turns out to have worms breeding in her intestines. Bailey enlists April's help to get Catherine and Richard back together, but it turns out that Bailey's similarity to Catherine is the key. During a press conference about the events on the plane, Maggie derives that something happened between Nathan and Meredith. Meredith tries to explain things to an angry Maggie and ask for her forgiveness. Alex's pregnant patient with pancreatic cancer from the Clinic returns to the hospital. Her cancer has metastasized to her spine, messing up the parents' plan for the future. The case strikes a chord with Amelia in particular.

Absent: Camilla Luddington as Jo Wilson due to maternity leave

April and Meredith discover that their patient has an inoperable heart tumor, which the patient already knew about. While the woman has made peace with it and has resorted to having as much good sex as she can before dying, Maggie can't let it go that easily. However, she comes to realize that there's nothing she can do. Inspired to do what's good for her in the moment, Meredith removes the tumor and post-it from her bedroom wall and takes Nathan home with her. Eliza and Arizona have sex after a whole day of anticipation. Richard has to second Eliza's statement that Ben has been playing it safe lately, while Stephanie lets her anger take over when a religious father threatens to sue the hospital for operating on his son's life-threatening tumor without his and his wife's permission. Andrew plans to tell Jo about his feelings, but she stops him since she already knows.

Absent: Kevin McKidd as Owen Hunt

Alex hires a private investigator and finds Jo's husband, Paul Stadler. He attends a conference where Paul is speaking, but he realizes that whatever he does will end badly for either Jo or himself and opts to let Paul go without a confrontation. Owen receives news that his sister was found in a basement after a raid in a rebel-led neighborhood. Amelia supports him and calls Teddy to verify Megan's identity and secure her transfer to Grey Sloan. Back at the hospital, the doctors are thrown for a loop when they discover that their half-naked car accident victims aren't a couple, but instead a woman who drove off the cliff on purpose to avoid getting raped. This discovery comes too late for Stephanie, whom the rapist has captured to secure an easy way out of the hospital. When the hospital lockdown traps Stephanie and Erin, a young girl wandering around the hospital, with the rapist, the rapist starts a fire to open the doors. Stephanie seizes the opportunity and sets the man on fire, but he drags himself towards gas tanks in a lab. Just as Stephanie goes to drag him away, the tanks explode.

Absent: Camilla Luddington as Jo Wilson due to maternity leave

As the flames rage throughout Grey Sloan, Bailey issues a mass-evacuation while Jackson and Meredith desperately search for Stephanie and Nathan. Stephanie, who is revealed to be alive, is forced to perform a surgery on Erin's leg, while the flames grow even bigger and looms closer towards the duo. Meanwhile, Owen and Amelia continue preparing for their journey, despite finding out about the incident at the hospital, to visit Owen's MIA sister, Megan. Back at the hospital, Stephanie is forced to go to extremes as she braves the growing flames on her floor, ending up in the staircase. Crawling towards the roof access with Erin in tow, Stephanie comes to the horrifying realization that her key card is missing, which is needed to open the door. Seeing no other option, she wraps Erin in a water-soaked blanket as she prepares to sacrifice herself. But just as the smoke reaches her, she sees that her key card is within sight and fights to retrieve it. As Stephanie and Erin at last enter onto the roof, Erin codes leaving Stephanie hysterical for help. As Stephanie is performing CPR while screaming for assistance, Ben leads a group of firefighters towards Stephanie's location, finally rescuing her at last. In the aftermath of the blaze, Eliza is fired by Bailey after an inquiry regarding the fire. Erin is alive and in recovery, and Stephanie is recovering from her burns as she tearfully tells Richard she's quitting. Nathan learns about Megan from Meredith who encourages him to reunite with his true love. Maggie is told by April that if she wants she could see Jackson. Owen and Amelia finally arrive at Madigan Army Medical Center as Megan's helicopter lands and she is pulled away on a gurney towards Owen, as he at long last comes to terms that his sister is truly alive.

Absent: Camilla Luddington as Jo Wilson due to maternity leave.