Endeavour Season 6 opens with Morse back in uniform and the disappearance of a child in Oxford.
Morse: It's not how things turned out, is it? It's never how these things turn out.
When Endeavour Season 5 ended with a promise of transfers to Thames Valley, most fans assumed Season 6 would find the show back where it started in the late 1980s. Not so fast. Only Strange wound up at Thames HQ and he's been shuffled off to do paperwork. Morse got sent to Woodstock CID, only to have the place close out from under him, and is now stuck doing uniform work. Thursday butted heads with his superiors over George Fancy's death and got busted down to Thames Valley's Castlegate station as a DS for his trouble. It's even worse for Bright, who got stuck in Traffic, forced to make safety spots for TV. (Ageism sucks, but that commercial is amazing.) Worse, the hoped-for romance between Morse and Joan isn't happening either. She's moving on with her life and training in the Welfare office.
The case that will eventually bring the gang back together begins with the disappearance of Ann Kirby, who went missing off the bus on her way home from primary school. Frazil is covering it, but she doesn't have Morse to turn to for info. He's dealing with drug addicts sleeping on church porches, a burglar who made off with some antique snuffboxes, horses going mising off of the Tingell farm, and a whole lot of regret. At least the horse turns up... leading right to Ann's body.
Morse, as a uniformed nobody, is dismissed by DS Alan Jago, who sneers at him to go catch the horse. However, the pathologist on the case is DeBryn, who gives Morse the lowdown. But any hope of him getting more info is dashed when the DCI turns up, and it's Ronnie Box. Even worse, Thursday is Box's assistant. (I don't know who should be more embarrassed here.) Thursday proceeds to shut Morse down when he asks about a possibly related cold case involving a girl named Emily, refuses to consider Box's fitness as an investigator, and responds to an overture to getting a drink in a tone that suggests he has no intention of ever doing so.
But Morse won't be stopped. He chases down the church junkie, Stanley Clemence, only to discover he's got Ann Kirby's satchel — notably without the copy of Black Beauty she was reading on the bus. Box is ready to wrap this up, using Clemence's withdrawal as a way to get a false confession. But Thursday is far less comfortable. He found Stanley as a toddler, witness to a crime scene where his mother was killed by his father, Philip. Turns out Joan's new boss at Welfare, Viv Wall (like the bricks that are about to come down on your head!), is also on Stanley's side, ready to go to war over his treatment, as he is 17 and still a minor. (Listen, at least Joanie questioned Morse's mustache when she finally sees him again, and Box's sexual harassment is shut right down when he learns her last name.)
While Box is running into a Wall, Morse is quietly checking the places Stanely worked, including the Skynners' farm as well as Tingell's, who was a childhood friend of Stanley's dad. He also checks the drug den where Stanley slept, and looks into the original Clemence case for good measure. But something funny is up. When Morse searches Clemence's place, he finds a bag full of drugs and a diary. When Thursday comes by a day later, on the same track, the bag has an added bonus: the missing headband from Ann's hair. But Clemence can't be questioned; he's escaped. Worse, another girl has disappeared, Rosie Johnston.
Box is convinced it all adds up, but Thursday isn't — and not just because Morse admits that he searched the place, with no headband to be found. Apparently, the exact thing happened in the original Clemence case. Thursday searched, but couldn't find the murder weapon, which then turned up, all of two days later, in a place that had literally been empty before. Thursday convinced himself it was all on the up and up at the time, but he's starting to doubt, helped along by Morse, who noticed things didn't add up either.
Eventually, Morse finds Stanley, dead of an overdose, in the church where he's hunting down the missing brushes from the father's case. DeBryn says the drug was spiked with something that's been taking out junkies left and right lately. (Whatever it is sounds like it might be part of this season's larger arc.)
Morse finds proof Philip was the killer, though hung on planted evidence, but Box was wrong about Stanley. Ann's death was an accident. Skynner's wife had hit her with their car while Ann was walking home, having exchanged her books at the local mobile library. They deliberately placed her body where she could be found, and loosed the horse for good measure. The real headband is in the car. The one Thursday found was planted by Box, who pleads with him to stay quiet, admitting he knows the older man should be running the joint. Gunshy from being busted down, Thursday acquiesces.
Meanwhile, Bright and his traffic team find the kidnapper from the fair — of all people, the man who reported his snuffboxes missing — Dr. Sheridan. He claims the half dressed photos of young girls they see are by Charles Dodgson (Lewis Carroll) until Morse realizes the statues in the background are ones Sheridan owns. Rosie is found safe and Sheridan's "daughter" turns out to be Emily, solving the cold case as a bonus. It's enough for Strange to get Morse a promotional transfer to Castlegate. He'll be working for Box now, but at least he and Thursday are back are together once more.