This is a completely original scenario, spanning the period from January 14th to March 3rd before the game takes place.
Narration starts in the third person, following Yukari. She's at Ouba during a wroship service. Yukari and Tsuzuriko chat before Tsuzuriko gets told off by a teacher, then both listen to Orihime's speech about how they must lead pure and proper lives in this postwar era blah blah blah in the new term, then head off to class.
In the Fujigumi classroom, Kusaka comes and announces that although there are no classes that day, they're going to recieve a lecture from the head second-year teacher (a female teacher who doesn't appear in the game) about leading proper school lives.
The teacher snaps at Touko, who's looking out the window, and Touko answers her pretty bluntly, so the teacher orders her to stand. As soon as she does, Touko collapses, bringing Mizuhara running over to her. The teacher accuses her of faking, but Yukari, who's been watching the whole time and sees how pale Toko is, intervenes and offers to take her to the infirmary, since she's the class health officer. Mizuhara of course tries to go along, but the teacher won't let her.
Yukari is worried about Touko, but she says she's fine, just having a bout of anemia. She tell Yukari she can go back, but Yukari insists on accompanying her until Akazaki gets there. Nene comes and tells Touko to rest, and Yukari that she should just stay there with Touko for a while since the day's almost over anyway.
By the time the bell for the end of classes rings, Touko is looking a little better, so Yukari gets up to go. Mizuhara of course has come racing into the infirmary to Toko's side by this time. Touko tries to be calvalier and says it's just because she didn't have breakfast, which Nene chides her for. As Yukari is thinking about how Touko has a mysterious charm that she never noticed before, even though they're both in art club, Mizuhara basically shoos her away so she can have codependant alone time with Touko, so after Yukari heads to art club.
In the art room, Yukari finds Nishizono Yui (who is very bright and genki in the manner of Tsuzuriko without as many nonsequiters). They talk about their club activities - the art club didn't meet during the break, so the members were supposed to draw at home instead, but Yukari didn't have time to; she was busy at home during New Years because of her lazy brother who didn't do anything to help. She mentions that she's gotten used to it now that her parents have died, and Yui comments that she's in the same situation. Ayumu, who has the day off from practice, shows up to see Yui. We learn that she's (ahem) very popular with her seniors on the kendo team. Yui teasingly asks Ayumu to model for her in the nude, and Ayumu jokes that she's too expensive
Yukari laments that she didn't have any time to sketch any snails at least, and then starts geeking out about bugs to the bemusement of Yui and surprise of Ayumu.
Yui, who's not a fan of bugs, tries to shut her up. They agree that they'd like to sketch outside more once spring comes, prompting Ayumu to mention that she just say Touko sketching out in the schoolyard. Yukari asks if Mizuhara was with her, and when Ayumu doesn't know, Yukari starts wondering about her bring out there alone in the cold after her attack that morning. Kusaka comes by with a handout he forgot to give them in homeroom, and Yukari offers to take Touko's to her. (Kusaka doesn't talk to Yui or react to her presence at all in this scene btw.)
She grabs some chuukaman from Nakamuraya on the way to the detective agency. Finding him out and the office a mess as usual (he's basically been living there for a large part of the winter), she resignedly gets to work cleaning it up. Just as she finishes, Reiji arrives.
The scene switches to Reiji's POV, and Yukari chiding him for being such a slob. He kind of brushes her off, but thanks her for always being there for him. She rewards him with some of the chuukaman she bought, then asks him how work's going. He says it looks like he's about to close his current case, and when she worries about his safety, replies that he's fine; he mostly gets mundane job requests and missing cats and such, although the possibility of encountering danger on a case is definitely not zero. He heads home with Yukari for a change, not having had time to do so much since the year started, and Yukari cheerfully makes him carry his dirty laundry from the office home so she can wash it.
Reiji thinks to himself about their home life without their parents, who died in a plane crash a few years ago. He has a bath and rereads a book about the Gallic Wars in his room until Yukari calls him for dinner. Reiji does some DEEP thinking after they eat about how murder and lies have always gone hand in hand, ever since the time of Cain and Abel etc. (We also learn, I think, that he and Yukari are living in relative luxury now because of the consolation money they got when their parents died.) Yukari comes in to say goodnight. Before he goes to sleep, he realizes that tomorrow is Sunday, so he can't go to the police station to get help on his case, but figures it doesn't matter since the case is as good as solved.
The next day at his office, Reiji thinks over his case, about a murder that occurred at a construction site. He muses that postwar Japan has become pretty dangerous, thought it's not all bad since it helps keep him in business.
Evening of the 18th. Reiji comes home to find Yukari worried about one of her senpai in the art club, who didn't return home that night. Reiji thinks it's just a standard teenage runaway and the police will work it out, but Yukari still seems upset over it, so Reiji offers to investigate it for her.
On the 19th, you can choose to go to Reiji's office, where he thinks about the factory murder case, Inokashira Park, where he sees what he thinks is a man throwing something into the pond (somehow related to the case; the park is near the shooting site), or Moon World, where he chats with Kyoko and she mentions that she's planning on taking on the daughter of an acquaintance as a new employee soon (you also learn that her husband, who I think it says served together with Reiji in the military, died seven years ago in a traffic accident, and that she took over running Moon World after him).

In the evening, Uozumi show up at Reiji's office with some files from the police department he wanted to see concerning the factory shooting case. When Uozumi wonders whether they'll actually help him catch his perp, Reiji says he doubts it; Uozumi demands to know why he had him bring them all the way over here, then, and Reiji is all "lol I forgot". They discuss the case for a while, and before he leaves, Uozumi asks Reiji if he'd mind taking on another case. He wants him to help investigating a phony religion that's been swindling its followers (probably the Koizumi Kei's dad ran), but Reiji declines and suggests he pawn it off on Takashiro instead; he's been looking to take on less dangerous cases like that now that he has a wife and a baby on the way.
Next, we get an angsty Mizuhara POV monologue about how she hates everything and everyone, but especially her mother, but because you-know-who is always by her side she can live on.
We now skip ahead to February 28th, back to third-person, where Uozumi has been called out to Inokashira Park early in the morning to investigate the body dumped there at the point-and-click crimscene (just a pair of arms and legs wrapped in black cloth, which must be Yui's). They estimate from the growth of the maggots that she's been dead for at least two weeks. He thinks that this came right as they solved the shooting case; the motive was money, just as he'd thought, etc., and thinks about bringing Reiji in on this one too.
Uozumi stops at Moon World on the way back, and is kind of hilariously tongue-tied around Kyoko as she tries to make conversation.
POV scene of the murderer going to work on a black-haired girl with glasses (Koizumi Kei) and inserting the black egg into her body.
Final scene takes place on March 2nd, where Uozumi discovers the second body in Tama Cemetary. Then we end with a trailer for the game, with a final frame of the title on black with Touko saying "Kara no Shoujo".