The twelfth and final season of NYPD Blue premiered on ABC on September 21, 2004, and concluded on March 1, 2005.

Notes Bale announces his mandate from the department to make the "rogue" 15th squad reflect "today's policing" and insists on micromanaging the details of every case, which causes friction with the detectives.

Following a lead developed by Medavoy, detectives find that the kidnapping was staged by the victim, and his conspirators killed his girlfriend, who was the young woman in the closet.

Notes Andy attempts to pull a drunken John Clark from a bar and is shot by an unseen assailant.

When he returns to the squad the next day, three AA "friends" confront him based on an anonymous tip they received and Andy has difficulty making them believe he had not been drinking.

Notes After being brought up short by both Bale and Baldwin, Clark reassesses his recent behavior and makes a tentative move to mend fences with Sipowicz.

A boy is molested by someone driving a church van and Ortiz and Murphy have to deal with a cop whose personal experiences impact his behavior on the case.

Notes While investigating closeted gay men who have been beaten and robbed, Andy finds Bale's credit card in the suspect's home.

Notes A young pregnant woman is murdered, and the detectives find that the father is a bigamist whose two families hold the key to solving the case.

ADA Munson is initially angry at Clark over Carly's return but apologizes when she notices the change in his demeanor.

Notes Andy and John Clark investigate the murder of a successful immigrant restaurateur with a taste for young girls.

Greg and Baldwin probe the murder of a public relations consultant whose clients included a famous, paralyzed former cop.

Notes Sipowicz and Clark investigate when an elderly millionaire whose wife is more than 50 years younger is found smothered to death.

Medavoy and Jones look into the murder of a State Supreme Court judge's elderly mother at a retirement home.

Notes A U.S. Army recruiter is shot to death and Clark suspects the brother of a soldier killed in Iraq.

Medavoy and Jones investigate the death of a homeless man whose body was found dead in a dumpster and find a connection to Murphy's first case after being assigned to the 15th precinct.

Clark and Jones become partners and investigate the beating death of a woman whose newly religious husband owns a jewelry store.

Notes Bale is hospitalized and his temporary replacement is more interested in playing golf than running the detective squad.

Andy questions his decision to take over as detective squad commander after top brass try to stop the investigation of a rich and powerful murder suspect.

Medavoy stops by while on a sales call and realizes that organizations continue to function even after one person leaves.