The Miniaturist draws to a conclusion as all the mysteries unravel, and Nella gets a happy ending of sorts.
Marian: To fight them in the open is to invite certain defeat.
When we last left our 1600s drama, Marian had been revealed to be with child, preparing to poison herself in a misguided abortion attempt, while Johannes has fled the country in fear of Franz and Agnes reporting his gay lifestyle to the authorities. But even though our heroine, Nella and her maid Cornelia are only putting the facts together, it turns out our Miniaturist has been trying to communicate this all along. The cradle was literally in the first package Nella received. And when Cornelia lifts the skirt of the Marian doll, it turns out there's been a baby strapped to it the whole time. Perhaps most creepily though, the sugar Agnes holds is rotting, seemingly of its own accord. What witchcraft is this indeed?
Nella once again behaves like a woman out of time. Much like her response to her husband, which is to accept his sexuality as simply a given, instead of running home and reporting him, like anyone her age would have in that era, she seems to have completely forgotten that having a baby out of wedlock is literally the worst thing any woman can do, and moreover Franz can't just swoop in and approve of Marian having his child since he's, you know, married to someone else. But all this is basically moot, as Johannes apparently dilly dallies his way out of the city and winds up caught at the docks when his boyfriend, Jack, turns him in. Nella has to bribe her way into jail to see him and already has a plan brewing, after inspecting how the sugar is doing.
Marin is already wise to Nella's idea of using her kid to pretend to be Johannes, but she's not so willing to give up the child or pretend to be an auntie. Turns out Marin hasn't admitted to the real truth: It was her who turned down the marriage proposal, not Johannes. (This makes way more sense. Johannes doesn't seem conniving enough to have done that without Marin's approval.) She didn't want to give up her freedom and become anyone's wife. And the child isn't Franz's anyway.
At least Nella is moving and shaking. She sells some of the sugar to the local cookie and cake bakers down the street with the hope if it moves, they'll buy more. Johannes attempts to sneer at the money Nella brings him, causing her to snap and tell him the truth about Marin turning him down, and suggesting he come round and ask her himself. At least when he does Marin won't be pregnant anymore. She conveniently has the child in between trial day one and day two, with Nella doing the attending honors. And then she conveniently dies in time for us to learn the truth of the father: Otto! So much for Nella using the baby proving Johannes is the father and straight.
Nella: What if we have a child, to prove the lie?
Johannes: Where are we going to get one of those in a couple of weeks?
Johannes trail is a show trial, of course, with Jack using all his acting skills to play act the victim, and fainting dead away when Johannes calls him out for having a wound far older than he claims. But the interesting discovery is that Agnes is playing with something during the trial...a miniature of her own. Turns out Franz bought her a cabinet back when they were married, and the Miniaturist has been sending messages in the same way she sends to Nella. The reason the woman closed up shop and ran is that Franz freaked out at the clues they were getting, and had her shut down. The miniature Agnes holds? It's a Nella doll.
Nella selling the sugar doesn't stop Franz from lying on the witness stand, condemning Johannes to death if he doesn't defend himself well. He does so in probably the show's best speech of the three episodes. It's good enough for a hung jury, at least on the first day. In the end, they find him not guilty on Jack and Franz's claims, but guilty of sodomy, which he admitted to in court. His punishment is to be drowned, naturally. Without knowing Marin is dead, Johannes requests Nella tell her not to come. At least he'll get that wish.
On the way out of court, Nella sees the Miniaturist and follows her, demanding answers. It turns out the girl has no answers. Some of her stuff is merely simple observation. (She knew Marin was pregnant because "I have eyes.") Some she cannot explain. Oh, and she has the parakeet, who comes back to the house. All she can do is tell Nella what the Wizard told Dorothy so long ago: The answer she seeks is already inside herself.
Those answers are perhaps not miraculously happy ones, but they're not bad ones either when one considers the reality of the situation. There's no magical rescue. Johannes is drowned, with Franz, forever trapped in a miserable marriage, bitterly sorry for his actions, deprived of his best friend and Marin. Otto turns back up and is introduced to his daughter and moves back into the house, much to Cornelia's joy. And Nella is free of both Brandts. There's no more Marin trying to control her. There's no more husband who will never sleep with her. She's a woman in charge of her own house, her own business, a free widow to find a man who will love her one day. Things can change, and now Nella is free to begin a life of her own. If that's not a happy ending for the time period, I don't know what is.