Bobby works with the firm of Cage and Fish to help in the defense of Marie Hanson, an apparent axe murderer who may have been Lizzie Borden in a past life. Ellenor discovers that her new boyfriend is the crooked chiropractor treating Rebecca, while Lindsay and Helen discuss Helen's future with the DA's office.

The crossover starts on Ally McBeal S01E20 The Inmates (I).

Bobby is hit by a car while his mind is involved on other matters. Meanwhile, Ellenor becomes disillusioned with the law when she comes to the realization that underhanded behavior has become second nature to her. Eugene defends a young man on murder charges. Bobby visits his father. Rebecca shocks the firm when she announces she's passed the bar exam.

Rebecca is faced with an ethical dilemma in the days leading up to her swearing-in ceremony; turn in a client she suspects of being a serial killer or fulfill her legal obligation. The firm prepares to defend itself against Tommy Silva, naming Jimmy as lead counsel. Bobby prepares to defend a babysitter against charges that she shook a baby to death.

Eugene battles his ex-wife Sharon for custody of Kendall. Sharon claims Eugene's profession and questionable tactics are sending the wrong message to their son. Helen prosecutes a young man for stealing a girl's car, but begins to doubt the alleged victim's story when the accused makes a very credible witness. The witness claims she was car-jacked. The accused adamantly maintains that the girl loaned him the car. Rebecca represents a psychologist fired from his job after suffering a head trauma that left him cross-eyed.

Tensions flare when the 'male nun' starts infiltrating the office. Ellenor buys a gun for protection. Rebecca suspects that a wealthy man has bought a client's guilty plea.

Tempers flare over a particularly tough case. Bobby defends old cling/drug dealer Eddie against the murder of an addict. Eddie claims it is self-defense. D.A. Helen brings the coroner to testify that it wasn't. The coroner's testimony is damaged by prior odd behavior. Eddie attacks Helen to try to force the judge into a mistrial. Bobby & Swackheim nearly come to blows. Each of the participants, Bobby, Helen & Swackheim, express their outrage with the legal system.

Dennis Mills maintains his innocence. The firm continues the trial, striving against all odds to exonerate Mills.

Eugene is disgusted by his client, a homeless man accused of murdering a woman and raping her corpse. Jimmy represents an old friend who's being sued for notifying employees that one of their co-workers has AIDS.

Bobby takes the Scott Wallace case to appeals, hopefully proving that prosecution witness Kyle Barrett perjured himself. Helen faces Rebecca in the courtroom in an emotional case when an abused spouse claims that she was mistaken in identifying her husband as her attacker. Bobby and Lindsay announce that they're expecting a child but Lindsay suspects she may not be the only pregnant woman in the office.

Tensions at the firm are at an all-time high when Bobby is tried for the murder of William Hinks. Bobby is acquitted, though there is little to celebrate when a mysterious cassette recorder is sent to the office. Lucy and Rebecca hear Hinks' voice on the recorder, just before it triggers an explosion.

Helen is enraged by Richard Bay's execution and determined to punish Jackie Cahill and all other responsible parties. She makes a deal with Cahill, offering him immunity on Bay's murder plus the added bonus that she won't announce that he's a snitch and release him into the general prison population if he gives up the shooter. He agrees. After the shooter has been killed by police, Helen reneges on the deal, claiming Jackie hasn't fulfilled the terms of the agreement. Jackie's lawyer protests and drags Helen into court. Meanwhile, Rebecca and Jimmy defend a man on charges that he strangled his wife. Rebecca is adamant about the man's innocence, arguing that the only reason he's being prosecuted is because he was stunned by his wife's death and gave the investigating officer erroneous information. Rebecca and Jimmy are shocked to later learn that their client has a history of strangling both women and chickens.

After promising the mother of a murdered teen that he'll find the drive-by shooter responsible, ADA Lowe adopts a “whatever it takes” attitude towards the prosecution of the young gang member he thinks did it—who is defended by Ellenor. Meanwhile, Lindsay is moved to help a mentally retarded man find the daughter he lost touch with years ago as a result of being wrongfully incarcerated for over a decade.

Eugene and Rebecca go head-to-head with Helen Gamble on a case involving a father accused of an unthinkable act of child abuse. Meanwhile, ADA Mitchell Wheeler, who previously made an indecent and unethical proposal to Ellenor, returns, this time with a different kind of offer for her.

Lindsay stands trial for shooting Lawrence O'Malley, who became obsessed with her after her firm defended him in his murder trial.

The strain of Lindsay's incarceration begins to affect her marriage and she lashes out at Bobby. Meanwhile, a zealous law-school grad who seeks to join the firm has a run-in with Ellenor; and Jimmy is embroiled in a 16-year-old child-kidnapping case that hinges on lawyer-client confidentiality.

Political, religious and moral issues surface in a trial involving medical research. Also, Lindsay, now on her own, defends a client whose singing gives a neighbor the blues.

Bobby has been benched due to his erratic behavior, so Eugene must take his place as lead counsel in a controversial murder case. Meanwhile Lindsay defends a killer, against her own better judgement, and Jamie is placed in a compromising situation involving a judge

A crazed fame-seeker takes CBS CEO Les Moonves hostage in a ploy for TV time to be negotiated by Jimmy, also a hostage.

Eleanor defends a man accused of killing his wife and unborn son. He contests that it was suicide. Eugene and Jimmy defend a woman who shot a crack dealer on her street. Alan Shore comes to Eleanor looking for a job after he was fired for embezzlement. He is given a case where a woman files charges against a homeless man who ""Halle Berry'd"" her (came out of nowhere and kissed her). He uses insurance fraud to coerce her into dropping the charges.

Fireworks erupt at Dr. Stewart's trial when shocking testimony is elicited from the defendant's strong-willed mother, a conflicted priest and a crackpot.