Miss Scarlet & The Duke began with the disappearance of Henry Scarlet, Eliza's father. Despite knowing her father's drinking habits, a gut instinct drove her to tell Duke, only to have him scoff at her concerns. Eliza's instincts were right; her father was dead, though of a heart attack, natural causes.
But there's an eerie similarity this week, as Ivy arrives to see Duke. Like her father before her, Eliza went out on a case and never came home.
Stirling: Formal dress, obviously... No kilts.
Last week's episode ended with a minor cliffhanger, as a picture falling off the wall revealed a hole containing Henry's final casebook. According to Ivy, whatever Eliza read caused her to rush off. Duke is currently dressed for dinner, an event Stirling has ordered him to attend, and desperately wants this not to be an emergency. But he can't ignore it. Tracing Eliza's movements takes him first to Rupert, where Herr Hildegard and Tilly are already visiting, then to Potts at the morgue, who complains bitterly about her coming by.
At her office, Duke finds himself consulting Henry's ghost the same way Eliza does when she sits at her desk. He also sees the casebook and finds the imprint of the page Eliza tore out: "Woolwich Prison, Cell 99." The prison was closed for years, but there's a voice yelling for help even before Duke arrives. It's Eliza, of course, locked into Cell 98. Cell 99 doesn't exist here; it's in another wing, one she hasn't found. Duke attempts to break her out. But their bickering gets to him, especially faced with missing his dinner with Stirling.
He almost leaves, declaring he's teaching Eliza a lesson about the importance of his job, which he needs to keep, whereas eventually she'll marry and give up detective work. It's a feint; he's gone to find the keys, figuring to let her sit and stew while he does. But he doesn't get far. Eliza didn't lock herself in; someone released the door. The thug who did it isn't about to let William leave either. Duke manages to knock out his would-be assailant, though not before getting his arm broken. (So much for his jacket or dinner.) After getting back to Eliza and letting her set his arm, the two head out, only to discover the attacker is awake and armed.
The two work together to defeat him, with Eliza distracting the man so Duke can punch him out. But as Eliza gazes down, she recognizes the thug. He's the one who claimed to be "Dr. Edwards," the man who found Henry's body and diagnosed the heart attack. Duke searches the man's pockets and finds the key to Cell 99. Eliza starts trying keys to get to the next wing and find out what's there, as the assailant, whose name is Harwood, wakes up and warns them the real heavy is on his way. It's an actual giant of a man, Garm (Roland Czaczyk), and once again, Eliza and Duke have to work together to escape.
Once away from Garm and wandering around the bowels of the prison, their bickering finally makes enough noise that someone starts shouting for help. It leads them to Cell 99, where there's a massive counterfeiting operation. Inside the cell, they find Nathaniel Caine (Rory Mullen), a career criminal forger who insists he was kidnapped after trying to go straight and forced into making thousands of pounds worth of fake bills of exchange (£68 thousand, all told). Recognizing Eliza's last name and stating he knew Henry, Caine says he'll turn states if they keep him out of prison. However, before he can tell them who is behind the plot, gunshots ring out. A masked gunman takes out Garm and Harwood on his way to finish off Duke and Eliza and protect this racket.
The gunman is wearing a leather mask with motorcycle goggles and sporting an air-rifle and a long leather duster, hiding whether they're male or female. The first shot hits Caine in the chest, dropping him to the ground. With no way to escape, Eliza draws a gun on their attacker and announces she'll start pulling the trigger until one of them is dead. Considering how bad her last gun firing went, it's a bluff, but the attacker doesn't know that. Perhaps they decide they don't want to kill women or cops, or maybe shooting Caine was enough, but the figure backs down and slowly slinks off.
Duke calls into the station, bringing Frank in to search the place, but the gunman has gone. Duke can now claim credit for uncovering and exposing a giant counterfeiting ring. It's a feather in his cap Stirling cannot sneer away, though he's displeased when Duke insists on police protection for Eliza. Duke responds by pointing out to Stirling Eliza cracked the case and that she's quite helpful to the department, shutting the man's bigotry down.
It kills Duke's chances of promotion, but he's got his team of Frank and Honeychurch and will be fine. That said, he still wants Eliza off the case. Not because she's not capable or because he wants the glory. These men murdered her father and went out of their way to make it look like a natural death. They also delivered his body home: they know where she lives and the layout of her house. However, it may be too late to keep her safe. Frank reports Caine is talking and crying out in fear of someone coming for him: a Jamaican named Moses.
Is Eliza's assistant only working for her to keep tabs on her? Unfortunately, Caine won't answer. As the episode ends, the masked gunman reappears and murders the witness in his bed.