Jo Mills was planning to take time off work, but then she agrees to defend a man who escaped trial sixteen years before after he was charged with attempted murder. Jo is partly attracted to the case because she recognizes two of the detectives who are mixed up in it.

Deed has an environmental case before him, in which a company operating a large-scale waste incinerator is accused of damaging people's health by air pollution. Jo Mills represents the parents of a damaged child, but is losing. Then it comes out that the company deliberately hid a fault at the incinerator which made its emissions far worse. Meanwhile, Rufus Barron comes up with evidence to support the claim that Neil Haughton took a bribe on a defence contract. Then the evidence is lost, and Haughton demands that Deed should be impeached for unprofessional conduct.

An angry contestant in a TV show kills another competitor on camera, and the show's producers face charges of manslaughter in Deed's court. Meanwhile, Deed is pressing for an inquiry into the death of Rufus Barron, a man who had been accused of embezzling money from his employer, the arms dealer Sir Tim Listfield. Sir Tim becomes violent when Deed keeps questioning the 'accident' which killed Barron.

Deed's superiors want him out of the way, and they arrange for him to be called for jury service on a case which will not be over quickly - a murder trial. In court, a teenage nanny from the Ukraine is accused of killing Baby Jonathan by shaking him, which she denies. As a juryman, Deed wants to see more medical evidence. Then he discovers a cross-over with a case of Jo's, in which she has evidence that the effects of the MMR vaccine could have led to Baby Jonathan's death. Meanwhile, Marc Thompson is asked to travel to South Africa, to give evidence about its child vaccination program - and Jo begins to have doubts about marrying him. After quarreling with Marc, she starts to see Deed again. But then she also quarrels with Deed, who still seems to have another woman in his life - one of his fellow judges.

Deed delves deeper into why funding for the soldier to sue the pharmaceutical company was withdrawn and makes ever more sinister discoveries. Then the forces of reaction move to stop him.

Deed has to judge a case concerning Jo's boyfriend, Marc Thompson. Marc wants to take the decision not to resuscitate a two-year old patient at his hospital who has a weak heart and is in a coma, if the child's heart stops again, but the parents disagree. In another case, Deed has to sentence a young thief, and the youth then dies in custody. All this brings back Deed's memories of his own traumatic childhood. He is spoiling for a fight and argues with Jo - who announces that she has decided to marry Marc.

In a case in Deed's court, his daughter Charlie is the junior counsel defending Henry Free - an animal rights activist charged with murder after a fire-bomb at an animal research unit killed an eminent scientist. Then Henry falls out with his leading counsel and asks Charlie to defend him - but Deed advises her not to. Part of Free's defence is that his group had been infiltrated by an officer of MI5, the British secret service, acting as an agent provocateur, and Deed is angry when Charlie reveals the officer's identity in court. Meanwhile, Jo is helping and encouraging Charlie - and she is back with her old flame, Marc Thompson. Deed is losing her.

After a young woman is battered to death, the mentally retarded Gary Patterson confesses and the police consider the case solved. However, Gary later withdraws his confession, leaving Judge Deed's court struggling with limited evidence.Meanwhile, Deed is also busy looking into a case about a multi-million pound mortgage fraud and comes up against a masonic conspiracy. The fraud case is due to go before a brother judge who himself proves to be implicated, and who commits suicide. In Deed's own court, the jury finds Gary Patterson not guilty, Deed asks who the killer was, and Gary says he witnessed the killing and knows the answer.

Deed's involvement in the case of a far-right British National Party councilor brings him to the notice of terrorists who decide to send a woman to kill him. When the assassin meets Deed, she has a surprise in store, but she still plans to carry out her orders. Meanwhile, The Lord Chancellor sends Deed to sit on an International Tribunal in the Hague, as the British government sees him as a mischief maker at home. Deed finds himself judging the case of a British soldier accused of war crimes by killing eleven Iraqi civilians.

In court, Deed has to judge the case of a couple who are fighting their local council over a police communications mast on the roof of the building they live in. Gilly Bridges has motor-neurone disease, while her husband Jake has stomach cancer, which they claim are connected with the 'tetra' mast. The incidence of both diseases in the Bridges' block of flats is many times the statistical norm. Jo represents Jake and Gilly Bridges, while Deed's former wife George appears for the defendant council. Then Deed receives an application from Rose Hussein, the English wife of a former government minister from Iraq. Rose believes depleted uranium used by the British Army in its tank shells killed her family - and she wants the court to establish the facts. Of course, the government doesn't want the case to be heard.

After a call girl is found dead in a skip, an Arab sheikh's chauffeur is charged with killing her, but the evidence points to the sheikh himself being involved in the murder. Unfortunately for Deed, the Arab ruler was in London to place a huge order with a British aircraft manufacturer, and pressure is piled on Deed by the British government, as well as by the sheikh's own. The plot thickens when counsel for the prosecution is also killed and Deed's lover, Jo Mills, takes over the case, and when he hears that Georgina Channing, his former wife, is engaged to marry Neil Haughton, the government minister fighting for the aeroplane order. Before long, witnesses disappear and the jury is being interfered with - by the British Government, no less. And then Deed gets an offer they think he can't refuse, when appointment as an Appeal Court judge is dangled before him.

Deed risks a constitutional crisis in pursuit of justice for a soldier?s family. Jo Mills asks him to review the withdrawal of Legal Aid funding in the case of the soldier, who committed suicide after being made ill by vaccines given to him by the British Army. Deed is reluctant, as the case has been heard and closed by another judge. His only course is to accuse the other judge of bias. When he does so, he causes consternation in the British government.

Deed questions an unpleasant prison officer closely about the death of Paul Settle, a young prisoner who was stabbed to death and then partly eaten by his cell-mate Ben Bradwell just a week before he was due to get out. The Judge is worried that Settle was black, while Bradwell was known to be a vicious racist. In another case, Deed comes up with a thoughtful sentence for a drunk driver who killed a child. Meanwhile, Deed and Jo seem to be growing apart.

Deed has the case before him of a man charged with killing a paedophile, but the jury find the defendant not guilty. After his acquittal, the man calls a press conference and sends out a message calling for similar actions elsewhere. Meanwhile, Marc Thompson, Michael's real father, arrives in England from overseas. This seems to end Jo's hopes of adopting Michael, but she starts dating the new arrival, sending Deed into a jealous rage. Deed then unwisely starts a new affair with a woman appearing in his court as a claimant in an action, and Jo decides to move with Marc to South Africa.

Deed has two difficult new cases in his court. In one, a woman with a brain tumour claims it was caused by using her mobile phone. In another, the defendant in a hit-and-run case seems unfit to stand trial.Meanwhile, in a continuing story-line from the second series, Deed's lover Jo Mills faces a disciplinary tribunal prompted by Sir Ian Rochester and presided over by Sir Monty Everard. Both of them bear grudges against Deed, and he rides to Jo's defence.

Jo Mills leads for the prosecution and Brian Cantwell for the defence when a British member of parliament, Alan Roxborough, is tried on a charge of attempting to murder his boyfriend with a frying pan. As usual, there is a conspiracy in the background to pervert the course of justice, which may be connected to Roxborough's opposition to certain British arms deals.Meanwhile, Deed goes into therapy and has a brief affair with his therapist.