Season 3 Episodes 5 & 6
"Climbing into Bed / You Never Know Who's Who"
A two-episode special: Ruzek's job is on the line after an ill-fated undercover op; the team investigates a band of rogue operatives.
To gain his trust, Ruzek (Patrick John Flueger) lets the target of an undercover operation drive his truck. Big mistake, as the target - with Ruzek riding shotgun - promptly drives through the front of a jewelry store, where a heist is already in progress. The target kills his (former) partners, takes the cash and jewelry, and gets away.
As he wasn't officially cleared at the time it went down, Ruzek's in hot water. He's relegated to desk duty while a special investigator handles his case.
After investigating the jewelry heist, the unit discovers it was an inside job. The thieves tunneled into the jewelry store after breaking into an adjacent restaurant, with the restaurant owners' son helping facilitate the operation.
But while the criminals are brought to justice, Ruzek isn't so lucky. As the investigation deepens, he is stripped of his police powers and forced to turn in his badge and gun.
As she preps to move into her own place, Lindsay (Sophia Bush) asks for Halstead's (Jesse Lee Soffer) help in finding a couch. After moving the couch into her apartment, they "test" it out; in the game of on again/off again, all signs point to on.
In the next episode, Burgess (Marina Squerciati) and a temp partner investigate reports of a suspicious parked car. Upon closer examination, they find that the driver is dead, the car is bulletproof and that the dead man is one Victor Cullen. After entering his house to search further, the unit finds a stash of over a million dollars in cash... and hundreds of weapons.
After linking the weapons to several unsolved crimes, the unit discovers a tangled web of deception and would-be espionage. Turns out, Cullen has been passing himself off as a CIA operative, and hiring men - unaware of Cullen's plot - to assassinate criminals the C.P.D. was unable to keep behind bars. After tracking down the pseudo-CIA operatives - and with a little help from Olinsky (Elias Koteas), who poses as a CIA agent - the unit is able to remove Cullen's team from the streets.
Desk Sgt. Platt (Amy Morton) is able to help Ruzek by interceding with the special investigator of his case. Ruzek is reinstated, and his case is closed.
Olinsky receives the results from the DNA test (to determine if he is Michelle's father), but decides to rip up the envelope before learning the truth.
Lindsay tells Halstead that their tryst on the couch was a one-time deal... but by episode's end they take their relationship public, holding hands and sealing the deal with a kiss at Molly's.