Martha enlists Alfred to help get the name of the new leader of the Raven Society.

In the wake of Esme's murder, Alfred is slowly pulled out of his depression by Ripper, who insists that an enemy of Alfred killed her.

Ripper sends Alfred to a witch who gives him clues to find Esme's killer. Lord Harwood's memory returns.

While Thomas and Martha visit Crowley's mansion seeking Patricia, Alfred closes in on Esme's killer, Captain Curzon. Arthur Pennyworth actively participates at a Raven Society meeting.

As Alfred hunts down Curzon with help from Bet, Lord Harwood plots his return to power.

Alfred is offered a way out of prison as the Prime Minister plots against both the Raven Society and the No Name League.

While Lord Harwood stages a coup, Alfred, Bazza, and Dave Boy help Thomas and Martha rescue the Queen from the Sykes sisters. Lord Harwood, Francis Gaunt, and the Sykes are arrested. Alfred is pardoned, but finds himself trying to stop his father from assassinating the Queen and Prime Minister.

Alfred buys three tickets to America from the money gained in the robbery. He tells Sandra he is leaving and breaks up with her. Prime Minister Aziz and the Queen recruit him for one last job against his will by blackmailing him with their knowledge that he had a fling with Melanie (Mrs. Gully). Alfred, Daveboy and Martha spring Lucius Fox from the Raven Union though it is a bloodbath. Alfred's mum reconciles with him and agrees to accompany him to America, if he abstains from further violence there. Lucius tells Thomas that Stormcloud is ready within a week and could kill everyone in London via a fear-induced chemical attack, but Thomas can do little but warn CIA upper management. Martha is revealed to be pregnant with Thomas' child. Meanwhile, Aziz manipulates Ripper (who wants his position) and Aleister Crowley against each other, which ends with Ripper confronting Crowley to threaten him, but ends up with Ripper drugged and institutionalized as he has terrifying hallucinations and cannot tell fantasy from reality.

With the powers of Gully, now called Captain Blighty, the League wins the civil war. Five years later, Alfred's security agency has expanded (including Daveboy and Bet Sykes), and several new people with powers emerge, whom they capture for MI5 Science branch - for whom Martha Wayne now works as an agent alongside Lucius Fox. Thomas and Martha have a 5-year old daughter named Samantha, who is babysat by Mrs. Pennyworth. Apparently, a nuclear crisis between Russia and the USA has just been averted (where Kyiv and Miami have been destroyed). Aziz is still prime minister of England. Sandra has gone on to have a career as a famous pop singer.

A doctor slashes the throat of a man with a scalpel and runs away. MI5 identifies the man as a CIA agent, but the Americans do not come forward, meaning the business he was in was top secret. A young woman named Jessica Thistle runs away from home, and her nanny hires Alfred to look for the missing girl. They find her in the ashram of Sister Susie, a hippie drug dealer, and extract her to return her to her parents. Meanwhile, Patrick Wayne, Thomas's father, whom he hasn't seen in years, shows up to reconnect with his family, alongside his girlfriend Virginia Devereaux. Martha suspects there is more to this visit. Bet Sykes is still on the trail of John Salt, who escaped from prison and is missing. She tracks down a former Raven leader and takes her and her husband hostage in their home, and when they resist, kills them and takes their baby, also finding a ledger with coded messages. The next day, Patrick asks Thomas' help in locating a Waynetech employee, Doctor Glubb, who ran away with priceless company secrets. Patrick asks for Martha's help, revealing to Thomas (who was unaware) that she is on active MI5 duty. Virginia chastises Patrick and threatens him to use more direct methods. When receiving a call that "the girl is in position", she gives the order to go ahead. The next morning, Jessica stabs her parents to death with a knife, then in a daze, walks to Alfred's home and collapses in the door.

Aziz questions Alfred about the murder, and it is revealed the nanny who hired him was a fake. Thomas confronts Martha about her working as a field agent, but she lies that her job is not dangerous. Thomas asks Alfred to work for his father and find Dr. Glubb. While watching over the comatose Jessica in the hospital, Daveboy confronts and kills a CIA agent who was trying to kidnap her. The fake nanny, a hired actress, visits Alfred's agency, having been stabbed on the way, revealing Americans hired her. Alfred and Daveboy move Jessica to Sandra's penthouse for safekeeping. Mrs. P. answers an advertisement in the papers seeking companionship, but leaves insulted when the man suggests they go to a hotel to have sex. Following up a clue about incense on the dead CIA agent's clothes, Martha infiltrates Sister Susie's ashram and questions her. She tells her that she was paid by the CIA to help run drug tests on her commune, but never saw any results. CIA agents show up and kill Sister Susie, but Alfred and Daveboy shoot them before they could kill Martha, who finds a hidden Waynetech camera behind a false mirror. Patrick talks to Thomas, and tells him the details - Dr. Glubb created psychotropic drugs for the CIA as part of Operation Lullaby State, which is developing mind control. Martha and Alfred realize Jessica killed her parents under the influence of the drugs, and something was used to trigger her - at the same time, when one of Sandra's songs is played at her flat, Jessica goes into a trance and starts to kill the partying people with a knife. She is shot at the last second by Daveboy before she could kill Sandra.

Below the fake MI5 front, Lucius visits the people with special abilities kept there. Gully, feeling down and caged, escapes using Fox to open the elevator for him with the retinal scanner. Alfred is contacted by MI5 to bring him back. Martha and Thomas exchange information, and Thomas talks to Patrick who is alerted to Martha knowing about the CIA's involvement in Operation Lullaby State. Feeling responsible for Jessica's death, Daveboy attends her funeral, causing a scene when trying to make a speech while drunk, but impressing an attending Sally Prufrock. Alfred finds Gully in a betting shop, and manages to mollify him, then disable him with a killswitch on the back of his armor. However, the patrons, angry at losing a bet, attack them to try and sell Gully's armor. Lucius arrives, giving Alfred the time to disarm them. Gully reveals he is still in love with Melanie, and wants to escape and find her. Alfred finds out his mum lied to him and went on a date. While at a playground with Mrs. P. and Samantha, Martha is approached by Dr. Glubb. He tells her he wants to work for MI5 in return for money and protection from the Americans. He also reveals he tried to make the same deal with the Thistles, who were murdered before he could complete it. Before leaving abruptly to escape the CIA, he warns Martha that Patrick Wayne is not the one she should worry about. Virginia, revealed to be a CIA agent, sees Martha leaving and authorizes an operation to tie up loose ends. While talking with Thomas, she drugs him and then operatives carry him away, to the impotent protests of Patrick. Alfred visits Sandra and comforts her. Thomas returns seemingly unaware of anything happening, however during dinner he gets a phone call that starts playing Sandra's song to him. Thomas hallucinates that Martha is a sadistic prison warden, and attacks and stabs her, but Mrs. P. knocks him out before he could kill her.

Thomas is arrested and imprisoned in the Tower of London, while Martha undergoes surgery to save her life. Patrick Wayne hires Alfred to break his son out and send him back to the USA, without Virginia's knowledge, offering to pay a million pounds. Alfred tries to explain to Aziz that Thomas was under the influence of a mind control drug, to no avail. Dr. Glubb, unable to make contact with Martha, is offered a deal by a mysterious person via a phone booth. Using a grappling hook gun and automatic lockpick developed by Lucius, Alfred and Daveboy break Thomas out of the Tower, becoming fugitives, but Aziz intercedes so that no charges are pressed. Daveboy attends a gallery exhibition at Sally's request, with whom he had a wild night of sex, meeting the flamboyant artist Francis Foulkes. Alfred takes Thomas to his home, disrupting an awkward date his mum was having. As Thomas refuses to leave the country without his family, Alfred confronts Patrick Wayne, soon finding out when Thomas bursts in that Virginia is his CIA handler, a rogue agent wanting to develop the mind control drugs further. She pulls a gun on them and Patrick reveals Virginia sent agents to kill Martha, but then the police burst in to arrest everyone, as Alfred called them in advance. The CIA agents find Aziz and the police waiting for them at the hospital, where Martha has safely pulled through the operation. Alfred is released and goes to his office, finding Sandra there, and they end up sleeping together. Meanwhile, a tied up Dr. Glubb meets his mysterious ally, a man wearing a Guy Fawkes mask.

Thomas' and Martha's relationship is strained due to the mind control assassination attempt, and they sleep in separate rooms. Patricia, Thomas' sister arrives unexpectedly, lodging up with the Waynes, and after Thomas tells her the events and how he feels about their father's behavior, this gives him the impetus to leave for Gotham to confront him, taking his gun. Prime Minister Aziz hires Alfred to act as security for Zahra Khin, the rebel leader of the former British colony Kalpoor who is in London for the summit but is not backed officially by the British government. After thwarting an assassination attempt on her life, Alfred takes her to his bar, where they unveil that her head of security was a traitor and deliver him bound and gagged to the Kalpoor president. Bet Sykes tracks down Mrs. Gaunt, now working as a doctor. Gaunt tries to dissuade Bet from revenge, and offers to take the baby from her, but Bet refuses. Mrs. Gaunt still tells her where she can find John Salt, but asks her to minimize the bloodshed. Mrs. Pennyworth reconnects with Roger, her date from last time, and they meet and dance together. Daveboy attends a new art exhibition event at Sally's request, organized by Francis Foulkes, where paint is poured on empty canvases and the guests. Sally convinces Daveboy to take a drug with her that she says will "link their dreams". It is revealed that Dr. Glubb works for Foulkes, who is the man in the V mask, and gave out the Lullaby State drug to select guests at the party for an undisclosed reason. Glubb warns him that without giving the subjects concrete instructions, it is not known how the drug will take effect, which is something Foulkes wants. Alfred accompanies Zahra to her hotel room and they talk and have sex, with her revealing that she is in London because she received information that her father who was supposedly assassinated 10 years ago is still alive. Alfred goes back to the pub and tells a still hallucinating Daveboy that it was them who kidnapped Zahra's father. Meanwhile, Bet Sykes tracks down and shoots an unfazed Salt multiple times, who rises back again, revealing he is now a cyborg as Bet is taken captive.

In a flashback, we see how Zahra's father was kidnapped, with a close friend of his betraying him to Alfred. In the present, Alfred and Zahra get ready to meet with the man who offers information about her father's whereabouts. In Gotham, Thomas arrives in Wayne manor and confronts his father, who does not try to excuse himself for his actions, but reassures Thomas that he loves him. Alfred confronts Aziz, aware that 10 years ago they kidnapped Zahra's father for MI6, and thus British intelligence would have him today, but Aziz denies knowing about any plot. Alfred threatens to break ties with him after this last job. Meanwhile, Bet is interrogated by Salt who reveals he too developed a supersoldier like Captain Blighty. After threatening the baby, he learns Francis Gaunt betrayed him, and orders Bet executed, but she escapes. Daveboy, still hallucinating, eats a letter Sandra gave him to deliver to Alfred. Alfred goes home for his spare gun and finds his mum and Roger together, which surprises him. After finding a room full of babies all belonging to Salt, Bet finds her baby, but is stabbed in the back by Salt. She triggers his extending spike implant through his heart, seemingly killing him. Alfred and Zahra meet with the contact, who tells her that her father is on a secret island prison at the Hebrides, and if she'd give the name of all her major supporters to the Kalpoor president, the British government would release him. Alfred disagrees, saying this is a trap and she was manipulated. The contact recognizes Alfred by his voice, and tells Zahra how it was Alfred who kidnapped her father, something Alfred admits. After a tense standoff, Zahra shoots the contact instead, but then breaks up with Alfred, telling him she never wants to see him again. A dying Bet leaves the baby on a bus to be sent to her sister Peggy, as she succumbs to her wounds. As the drug wears off, Daveboy realizes he cannot remember the last 2 days' events, as Alfred tells him they will go to the Hebrides to perform a prison break. In Gotham, Patrick Wayne leaves a bar, and a masked figure shoots him dead in an alley. The figure is revealed to be Thomas Wayne.