Last week's Miss Fisher's Murder Mysteries ended with Jack declaring his and Phryne's partnership over. That's why this week's cold open starts with Dr. Mac and Professor Bradbury (Lewis Fitz-Gerald), ushering in students to her last anatomy lecture ahead of the Medical Prize exam. Only, instead of the presumed corpse, they uncover fellow lecturer Prof. Martin Katz's body, with his throat cut open.
When Fisher arrives at the college, she see Amos Oliver (William Ewing) torturing Beatrice Mason (Andrea Demetriades), one of the student's from Dr. Mac's aborted lecture, as a third student, Charlie Street (Jared Daperis), intervenes. Once inside, Mac admits she didn't look under the sheet when she rolled up the body.
Beatrice: That's not relevant, Dorothy.
Then Jack walks in, escorted by Bradbury. (Awkward.) The key to the furnace room where the corpses are kept disappeared, so Jack has the students assembled for questioning. Phryne makes a beeline for Charlie, Bradbury's assistant. He points her to Katz's office, and Jack follows. Beatrice is outside, arguing with Collins she needs to grab her research notes. She's on the autism spectrum, (though the show never says so directly), and darts in after Jack and Phryne. Someone has been in ahead of them, attempting to open Katz's safe. Beatrice says it holds a 16th-century illuminated manuscript, The Book of Hours of Juana the Mad.
Geoffrey Spall (Nicholas Hope), the college treasurer, joins them, saying Katz changed the combination daily. Once opened, they find the book missing, save a single page. Beatrice grabs it and runs off. Fisher follows her and notices a trail of blood. It leads to the murder weapon, and the courtyard, where Katz's body was drained. Beatrice faints. Charlie leads everyone to the Vice Dean's office. Fisher notes, when he pulls out a banket, something falls out. She sends Collins to follow him; it's the missing key to the furnace room. Bradbury insists the safe should have also held the skull to be used for the Medical Prize exam.
When Beatrice wakes up, Fisher realizes she's squatting in the Vice Dean's office, and asks the girl to stay with her, which she does, with all her research books. Beatrice enters through the back, believing someone who wants the manuscript is following. She copied out multiple pages, noting where things were altered, letters over-inked with red, but she doesn't know why. But someone wants her notes, it's why she lost her flat. It was ransacked regularly until finally someone nearly burnt the place down. She's not making this up. Butler discovers the pot of jam for her beloved sandwiches was drugged with sleeping pills, the hard way.
Charlie admits the key was among Beatrice's things, but he believes Amos Oliver did it. Oliver is a third-generation student whose father and grandfather won the Medical Prize. Amos is a cheating weasel who Katz was trying to have expelled. Jack brings Oliver in and is not intimidated when the kid responds his uncle is the Queen's Counsel. Oliver claims his alibi is Beatrice, who came to his rooms, desperate for sex. Beatrice counters Spall told her Oliver wanted her to come to his rooms, so he could apologize. But when she arrived, she was exhausted and slept heavily.
That night, someone breaks in and attacks Beatrice, stealing her notes. Fisher tries to catch him but is thrown to the floor. She does get his handkerchief, which smells of Spall's pipe tobacco. Jack is furious and has the man's office searched. Fisher gets a look at it, and her theory the Book of Hours holds a code becomes more likely as Jack turns up Spall was a spy during the War, keeping surveillance on his colleagues, and the drug in the jam was a truth serum. Though her notes were stolen, Beatrice has a copy of just the altered letters. Spall insists they mean nothing to him, and all but accuses Charlie and Beatrice of Katz's murder.
Collins finds the missing skull in the men's room. It matches the inventory number Bradbury provided, but Dr. Mac doesn't recognize the system. She takes the skull to make sure it's the right one. Charlie walks in, finds a letter in his mailbox, and leaves. Fisher follows him to discover a trail of pages from the missing Book of Hours, and a confused Charlie, who dug up the manuscript out of the dirt. Spall jumps out, accusing the kid of stealing it and pulls a gun, but Jack recognizes it's a set up and arrests Spall instead.
Spall tells Jack the police are out of their depth. Katz's murderer is still out there. Charlie shows Jack the note that led him to the book, which refers to Katz as an 'old coot" the same way Oliver did. When questioned, Oliver admits when Beatrice showed up expecting an apology, he thought it was Katz's idea. After she fell asleep, he went to have it out with the professor. When Oliver saw the skull on his desk and the book, he grabbed them, planning to cheat with one and blackmail Katz with the other. The kid is a cheating idiot, but he's too dumb to have killed anyone. With the book in hand, Jack, Phryne, and Beatrice crack the code, which involves double agents during the War.
Spall admits that is the message. But he didn't kill Katz; it wasn't until he heard the man was dead that he broke into the office, just ahead of Jack and Fisher's arrival to search it. But that's all Jack gets, because someone very high up calls to have Spall released. As for the skull, the numbering Mac didn't recognize is American. The skull isn't the test skull, it's of an African American woman, a college graduate. Its size and shape are like any other human, disproving biological inferiority in sex and race, on which Bradbury centered his career. Bradbury ordered Charlie to destroy it. Instead, the kid took it to Katz,and Bradbury freaked out and killed him. When Jack attempts an arrest, Bradbury runs. Jack and Phryne jump on a motorbike to chase him down, doing what they do best together.
Fisher, Mac, and Jack drink together that night, celebrating the first recipient of the Fisher Academic Award: Beatrice Mason. Best of all, Jack and Fisher are back together as a team.