Everyone in the ER is trying to cope with the loss of their colleague. The staff feels defensive toward the new Chief and her tough disposition. Gates and the new interns treat a bio terrorist, who has a lethal secret that endangers them all. Neela makes a great effort to get Dubenko back on the surgery staff, and gets help from an unexpected souce.

Sam's time is taken up by her studies for a pharmacology exam, leaving Gates feeling neglected. A school fight results in a stabbing, with Brenner treating the victim and trying to uncover the truth behind the story. Morris has a surprise for Neela. Gates gets locked in a stairwell with a quiet young boy on Halloween night.

Dr. Banfield is irritated when Morris takes Chaz under his wing and teaches him risky medical procedures; Neela is unhappy when Dr. Banfield undermines her authority with an intern.

Sam gets frustrated with Gates when he gets obsessed with finding a homeless war hero. Neela is upset at her intern after he gets the entire surgery department into a lawsuit. A husband and wife come into the ER after someone tried to burn down their home. Brenner loses his cool with a patient and it gets physical.

Morris' father arrives at the ER's doorstep and leaves him an unwanted package. Sam wants Alex to get off the ventilator as quick as possible following his accident. Meanwhile, a woman is in danger of being deported despite her high-risk pregnancy.

Alex is set to be released from the hospital. Doctors treat African-American brothers Curtis Bennet, 17, who has abdominal pain and 10-year-old Quincy Bennet who has a knee injury. Both were injured during a drug deal that went terribly wrong. There's still some residual tension between Gates and Sam. A female patient in police custody doesn't want to be examed by Morris. A 13-year-old patient named Anastasia messes with Neela's love life.

Morris tries to help a girl who was hit while riding her bike; Gates can't get over his feelings for Sam; Neela is flustered when Dr. Brenner returns from Australia.

Neela and Sam are shocked when they arrive back to the airport with transplant organs only to find that their plane has left them. Dr. Carter gets a surprise visit from an old friend while waiting for his kidney transplant. Dr. Banfield bonds with an abandoned baby boy that is left at the ER.