In the fallout of Izzie's decision to quit the program, the interns try to help Izzie come to terms with the death of her fiancA©, Denny. Meredith is forced to decide who will be the man in her future after her fling with Derek during the prom. Meanwhile, Dr. Webber is confronted by his wife after spending the night at the hospital; George asks an unlikely person for relationship advice; and Addison must find out which one of a group of teenaged girls is the mother of a baby found in a trashcan.

While Burke continues to recuperate in the hospital, his parents arrive at Seattle Grace to visit and end up meeting Cristina in embarrassing circumstances. The interns, as well as Bailey, lobby for Izzie to be re-admitted to the intern program. Meanwhile, Addison opts to take a day off from the hospital and spends the day at Joe's where she runs into both Izzie and a surprise visitor from her and Derek's past. Elsewhere at the hospital, a patient lives what she believes to be her last day to the fullest.

Finn and Derek continue to try to outdo one another in order to win Meredith's heart. Derek woos Meredith with once in a lifetime surgeries while Finn tries his hand at a romantic hospital date, all making it more difficult for Meredith to make a decision. With Burke's hand continuing to tremor, Cristina does her best to help him deal with his injury. As George and Callie's relationship continues to grow, Izzie attempts to visit the hospital for the first time since Denny's death. Meanwhile, Alex tends to a patient with numerous injuries.

As Addison works with Rebecca, a pregnant woman who needs to have a C-section but wants to give birth naturally, she begins to doubt her abilities as a doctor. The interns work with Shawn Sullivan, a car salesman who wants to return to his normal routine after he has surgery. However, when Shawn lights a cigarette that catches his face on fire, Derek and Mark argue over how they should procede with his burn treatment. Meanwhile, Burke continues to rehab his injured hands with the help of Cristina, gradually progressing from operating on chickens to operating on a corpse. Meredith goes into surgery after her appendix bursts and after surgery, she finally makes a decision between Derek and Finn. Elsewhere, Callie and George continue to discuss their relationship and Izzie meets a man who gives her the surprise of her life.

Bailey treats a young woman suffering from breast cancer while Derek begins to learn more about Addison and Mark's rekindled relationship. Meanwhile, the interns team up to defend a resident at a staff meeting, and Meredith and Addison stumble into an awkward situation with one another.

Cristina gets the once in a lifetime opportunity to scrub in on a rare humpty-dumpty procedure, much to the envy of the other interns. Meanwhile, Alex begins to question his choice of surgical specialty and George and Addison work together to help Noelle, a woman pregnant with twins that are developing at different rates.

The Seattle Grace men pack up and head out to the Seattle wilderness for a camping trip. Back at the hospital, Callie and Addison work together on a pregnant patient who slipped and broke her arm in the shower and Meredith helps Dr. Sloan with a unique sex reassignment surgery. Meanwhile, Bailey becomes increasingly suspicious of Cristina and Burke and decides to confront Cristina. Elsewhere, the interns treat a 9 year-old who swallowed Monopoly game pieces.

George's family comes to Seattle Grace when George's father hurts his clavicle, throwing George into a frenzy. However, George's worst fears about his father's hospital visit are realized when the test results come back abnormal. As Meredith strives to have a more positive outlook on life, Derek and Addison work on finding away to have a civil relationship once again. Meanwhile, Richard attempts to work things out between him and Adele.

The ER is taken over by a horrific car accident and the trauma caused by the accident pushes and challenges the interns. Elsewhere, Cristina begins to wonder if she's doing the right thing by helping Burke lie about his hand condition and Izzie pushes the boundaries of her probation.

Burke and Cristina's relationship continues to be strained in the aftermath of Cristina revealing Burke's limitations due to the shooting. Meredith's half-sister, Molly Thompson, is admitted to Seattle Grace forcing Meredith to once again confront her emotions towards her father and sister. Meanwhile, Derek and Mark are forced to work together when two conjoined brothers come to the hospital to be separated.

After George's father's heart operation, Mr. O'Malley heads back to the O.R. for another surgery for his cancer. As George continues to worry about his father, Meredith's father visits Seattle Grace in order to see his newborn granddaughter. Meanwhile, Meredith discovers that Derek is having trouble sleeping, which is no fault but her own. Elsewhere, the interns treat an angry 17 year-old girl with severe scoliosis who has a poor attitude towards the doctors due to the several surgeries she has endured during her life.

Mr. O'Malley heads back to surgery in order for the doctors to operate on his cancer. Meredith deals with her emotions while her father is at Seattle Grace to visit his new granddaughter. Meanwhile, a woman has a breakdown at the hospital after having to give up something important to her. Elsewhere, Meredith continues to worry about Derek when he is unable to sleep.

While rumors about the chief's retirement begin to fly among the hospital staff, Bailey pushes for the creation of a free clinic at Seattle Grace. George uses sex as a way to cope with the death of his father, which worries both Izzie and Callie. Meanwhile, The interns treat a woman diagnosed with stage 4 cancer who has a complex Puritan past and Callie and Cristina operate on a runner in order to save his legs. Later, one of the doctors receives a surprising proposal.

With Izzie's inheritance money, Bailey and Izzie open the Seattle Grace free clinic and eagerly wait for their first patient. The lives of the doctors are put at risk when a patient's blood is found to be toxic. Meredith, Cristina and Izzie volunteer to risk their lives to save the woman after Derek and Burke's air-tight suits run out of battery. Meanwhile, Ellis, Meredith's Alzheimer's-stricken mother, has a change in her condition; George and Callie return to the hospital with surprising news; and Cristina gives Burke an answer to his proposal.

A horrific ferry boat accident challenges the interns, as well as the rest of the hospital staff, both physically and mentally as they all near their breaking point. Chief Webber has to assemble and send out a team to the location of the accident to help save the few lives that were spared. On location, Alex tends to a woman who was crushed by a cement pylon. Meanwhile, Meredith looks out for a lost young girl and George searches frantically for a woman's young son.

As the chaos surrounding the ferry boat accident continues, Derek frantically searches for Meredith, and is devastated when he finds her barely clinging to life. Cristina is also devastated when she learns about Meredith's condition. Meanwhile, emotions run high at Seattle Grace as family of the accident victims demand to know the status of their loved ones. In the midst of the trauma, Alex has trouble dealing with the death surrounding him; George searches for a missing 7 year-old boy; and Izzie is forced to take desperate measures to save the life of the man stuck under a car.

While Meredith's life hangs in the balance, the interns each have to grapple with the reality that she may not make it. Derek refuses to give up hope that Meredith will pull through, but as time passes, Derek begins to slowly break down. Cristina takes the possibility of her death the hardest, and refuses to accept that it could happen. As Bailey and Chief Webber work to save Meredith's life, Meredith is visited by figures from her past, including Denny and Dylan Young, both of whom try to convince her not to die. Elsewhere, Addison and Alex continue to work with their pregnant Jane Doe, who has no memory of the ferry boat accident or her life prior it.

The race for Chief of Surgery continues to heat up, especially when a new contender enters the race. Callie reveals a big secret to George, and when George ends up telling Meredith, Callie kicks him out, leaving George with no where to go except to Meredith's. Cristina and Burke's engagement suffers when a secret about one of Cristina's past relationships is revealed. Meanwhile, Derek treats an old friend; Alex and Jane Doe get closer; and Meredith has dinner with her father and step-mother.

George comes face-to-face with his father-in-law, but the circumstances of their meeting are less than perfect. Alex continues to tend to Jane Doe and helps her choose how the world will see her from here on. Meanwhile, the board interviews Chief of Surgery candidates, and everyone is stunned when Sloan emerges as a top candidate. Elsewhere, Izzie wrestles with the events of her drunken night with George.

When Izzie has to face her past, she turns to George for support and comfort. As Alex continues to work with Jane Doe, the two become more attached to each other. Meanwhile, Meredith and Derek begin to question their status while Cristina strives to repair her relationship with Burke despite her past history with Dr. Marlow that continues to damage their engagement.

As the interns study for and stress over their upcoming exam, the attendings suck up to the chairman of the board in order to become front runner for the Chief's position when he is admitted to the hospital as a patient. Meanwhile, Burke has a difficult time involving Cristina in the planning of their wedding, Addison and Alex get closer, and Derek begins to second guess his relationship with Meredith.

Addison, on leave from Seattle Grace, heads to Los Angeles to reconnect with old friends from med school. Back in Seattle, Meredith continues to bond with Susan, her step-mother, and Cristina, with the help of both her mother and Burke's mother, begins planning her wedding. Meanwhile, Derek performs emergency surgery on Ava (Jane Doe) and Alex continues to stand by her.

In the conclusion to part 1, Addison visits Los Angeles and continues to reconnect with her old medical school friends. In Seattle, Meredith gets closer to her step mother. Cristina deals with the pressures of her pending marriage, and reluctantly plans the wedding with her mother and future mother-in-law. Meanwhile, Derek operates on Ava.

The interns face one of their biggest challenges yet -- their first-year medical exams. Meanwhile, the interns must tend to three injured mountain climbers. Elsewhere, Callie becomes increasingly suspicious of George and Izzie and Cristina has trouble writing her vows.

A big day arrives for all -- Cristina and Burke's wedding and the interns receive their exam results. Meanwhile, Chief Webber's replacement is named and George and Callie make a decision about their relationship.