A female party-goer and rape victim claims self-defense after killing her attacker. Events take an unusual turn when they find out that the victim is a pre-operative transgender.

Detectives enlist Dr. Huang's help as they investigate the deaths of two high-school basketball players gunned down while shooting hoops in the gymnasium and the connection to an illegal marketing campaign by a major pharmaceutical company.

A female undercover agent for the DEA is raped and murdered, leading to a complicated investigation and the arrest of a suspect highly connected with a Colombian drug cartel. This is the toughest case of Cabot's career as she is faced with death threats on herself and her family along with pressure to yield the case to federal authorities.

A newborn baby is found dead in a gutter, sending the detectives on a hunt for the mother. She too turns up murdered, and the clues point to a serial child molester.

Benson and Stabler have trouble identifying a male murder victim in his 20's found in a pile of sheets in the West Village; they later suspect an outspoken minister who was in the process of flooding the victim with hate mail and death threats. When the activist's alibi checks out, the detectives turn their attention to a professor who objects to the victim's thesis on the failure of sexual re-education groups.

The discovery of a beaten infant leads detectives on a search for the attacker, who may be a pedophile. When the medical evidence shows the injuries were a result of shaken baby syndrome, their focus shifts to those closest to the child: her mother, the mother's boyfriend and the nannies.

After a young woman is found raped and murdered near a nightclub with five hundred dollars stuffed into her mouth, Benson and Stabler follow the fingerprint trail on the money to Attorney Jason Whitaker, whose sole responsibility seems to be handling the trust for the Duvall family. Soon detectives are convinced that Gabriel Duvall is their rapist, but don't have quite enough evidence to put him away. ADA Novak is working on both the case and a terrified former victim when she is brutally attacked in her office late at night. The crossover continues on Law & Order: Trial by Jury S01:E11 Day (II).

After the wife of a police officer claims her husband raped her, Benson and Stabler arrest the man and come close to believing his version of events when he attacks his captain. When another officer murders his wife and attempts to kill himself that same night, the whole force gets involved and soon realises that the two men both recently returned home from Afghanistan, where they were given the drug Quinium, an anti-malarial. With the reluctant help of reporter Sherm Hempell and a base doctor with an attack of conscience, Novak takes on the U.S. army. Stabler has trouble with the case because of his history in the marines.

After a dating service is linked to three rapes, Olivia goes undercover to ferret out the rapist and meets Mike Jergens, a surgeon who enjoys controlling the women in his life. The detectives are soon led to his girlfriend, Cora Kennison, but shortly after testifying in the grand jury hearing Cora marries Mike. After Cora attempts suicide, Mike fights her mother, Virginia, to unplug her feeding tube.

After sixteen-year-old Lauren Westley loses her unborn child due to a severe abdominal beating, her father's insistence that Lauren was raped leads detectives to the baby's father, but it isn't long before the detectives realise that Lauren was an active party in her own beating, and the two teens had found it necessary to take the steps they did because the abortion clinic kept putting off Lauren's request for an appointment. Novak faces a tough opponent in her own office when she and Branch disagree over the appropriate action to be taken against Wayne Mortens, the young girl's boyfriend.

Doug Waverly and Nick Pratt are charged with rape and murder in the disappearance of Canadian student Jennifer Durning after Nick's cousin, Jason King, claims that while he had consensual sex with her that night the other two raped her. A stray pubic hair leads Novak to Keith Willis, a drunk who was paid off by the boys to get Jennifer out of the hotel and who later saw the boys kidnap her, but Willis exactly fit to be a witness as his mind has gone after years of alcohol abuse. Jason King disappears. Although they are able to find a bug in Donnelly's office, they are not able to prove that it was placed there by Pratt or Waverly. Judge Donnelly is forced to dismiss the case against the two boys since there is no case without Jason's testimony.