Macy (Miguel Ferrer) and the rest of the coroners decide to take turns helping care for Jordan (Jill Hennessy) after her brain surgery. When Bug (Ravi Kapoor) does not show up at Jordan's to relieve Woody, (Jerry O'Connell) Nigel (Steve Valentine) gets angry and then realizes something is wrong. Woody and Nigel begin to investigate and find out that Homeland Security has taken him into custody and are accusing him of being a terrorist.
Jordan (Jill Hennessy) decides that she is ready to get back to work, but Macy (Miguel Ferrer) is reluctant because he feels it is too soon. After agreeing to take it easy Jordan finds herself thrust into a murder case and find herself back to her old ways. Everyone is concerned about Bug's (Ravi Kapoor) demeanor since his encounter with Homeland Security and wants him to open up about his experience.
Rush reopens the murder case of a 16-year-old girl after a prison inmate, bargaining for a reduced sentence, relates a conversation he overheard 22 years ago, intimating that the wrong man is currently serving time for the murder.
Rush gets a visit from a frail 75-year-old woman seeking justice for her dead son, the victim of a 1964 gay bashing incident. As Rush investigates, she discovers a former underground world in which gay men were forced to live like criminals.
After Jack and Bobby catch a steroid drug dealer they, along with Sue, interrogate him in order to catch other dealers in the trade. Meanwhile, the rest of the team sets their eyes on the brand new offices on the fifth floor.