6x1 – Episode 1
St. Eligius is reopened thanks to a new corporate owner, whose plans please Craig but leave Westphall wondering; Elliot is missing from the returnees; Fiscus finds the first patients; the Craigs' marriage seems to be headed for court.
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6x2 – Episode 2
A fantasy grips Ehrlich; the Morrison family is crowded by close quarters and a visitor; Gideon finds an error when he steps into Westphall's territory; a large man undergoes hypnosis for surgery.
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6x3 – Episode 3
Fed up with the changes imposed by the hospital's new owners, Dr. Westphall resigns from St. Eligius. As he quits, he moons Dr. Gideon.
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6x4 – Episode 4
A student nurse's lie comes back to haunt her; Warren wants better conditions for the orderlies; Craig's artificial-heart program improves as his marriage deteriorates; Wade's hostelry is filled with hostility.
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6x5 – Episode 5
Chandler takes on a patient whose problems may have to do with Mrs. Hufnagel; the Craig 9000 is implanted once the recipient is rounded up; Elliot is feeling gloomy on Halloween.
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6x6 – Episode 6
Ehrlich embarrasses himself at a conference; Gideon makes offers to Chandler, Morrison and Ellen Harper.
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6x7 – Episode 7
The hospital begins tests on the last candidates for the artificial heart; an archaeological team focuses on the present; Elliot takes a shot at surgery; Fiscus continues his winning streak in the ER.
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6x8 – Episode 8
Plans change for the Craig 9000. Rosenthal returns to the OR. Morrison's real life clashes with his new public image. A gaybashing incident leads to an understanding between Griffin and Brett Johnston. Ellen and Gideon start a relationship.
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6x9 – Episode 9
Morrison races to deliver the 100,000th baby at the hospital. Fiscus plans his last prank before turning 30. Craig attempts to deal with his feelings about his father by sparring. A man makes his final walk along Freedom Trail.
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6x10 – Episode 10
The artificial-hear press refuses to speak to the press; Auschlander wonders about his last days on Earth; Fiscus visits his father during his suspension; sparks fly between Novino and a man called Pee Wee.
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6x11 – Episode 11
Some are claiming credit for the Craig 9000 while others are questioning its value; Kiem helps a neighbor with nowhere to go; Brett Johnston decides to carry the burden of illness on his own.
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6x12 – Episode 12
Cameras capture the staff at work; Papandrao is worried that Ehrlich won't take her news so well; a man comes back to St. Eligius for an unusual procedure.
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6x13 – Episode 13
Kiem tries to help during street gang wars. Helen Rosenthal is deeply affected by the death of Bobby Caldwell from AIDS.
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6x14 – Episode 14
Siblings have different reactions to the possibility of having a genetic disease; Luther and Auschlander have a shot at performance art; Rosenthal's drug abuse worsens.
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6x15 – Episode 15
Craig and Gideon are both affected by death; Ehrlich is too busy with his work to spend time with Papandrao; Rosenthal feels pressure under visual scrutiny; Luther shares his thoughts on size with a big man.
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6x16 – Episode 16
Papandrao and Ehrlich share a loss; a pair of punks defend one's right to die; mystery surrounds a man who keeps getting blackouts; Craig learns how the mighty are fallen.
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6x17 – Episode 17
Friends gather to celebrate Westphall's birthday in New Hampshire, while Ellen, Craig and Lizzie question all the decisions they've made in their lives.
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6x18 – Episode 18
Surgeons are forced to work nude during an OR-infection study; a visitor lifts Auschlander's spirits; a dumpster dweller protests hospital waste; Morrison and Novino fight an infection in the ICU.
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6x19 – Episode 19
Ehrlich verbally assaults Craig; Griffin fails as a spiritual counselor; Elliot undergoes surgery; Rosenthal enters family therapy with little support; Gideon is made the victim of another high-tech innovation.
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6x20 – Episode 20
Craig returns to the hospital, while Rosenthal wonders if she can return to work as well; Brett Johnston's parents pay him a visit; Auschlander is asked to be a best man.
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6x21 – Episode 21
A fire starts at the Doctor of the Year dinner; Papandrao and her in-laws look for Ehrlich; Chandler is in for a surprise; Fiscus tries to figure out how to tell his plans to his mother; Wade is upset by her patient's bickering parents.
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6x22 – Episode 22
Third year doctors end their residencies. Auschlander tries to keep the hospital open but complications arise. Griffin places his trust in God. Ehrlich comes back from a soul searching surf safari. Ellen is offered a job in Cleveland.
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