Came across the idea of Mordred and Saber both being around for the 5th War and the fact that Shirou would effectively wind up being Mordred's stepmother, leading to this: Mordred's Oedipus complex. She already has the issues with her father (Saber), and with a "mother" like Shirou, it's easy to develop.
As they're living happily post-Grail War, Mordred isn't actually so happy. She doesn't actually want to build a nice relationship with Saber, but she doesn't want to bother with fighting when she expects to lose. Instead, she hits on another strategy: Saber loves Shirou, so Mordred will take him away. It's obvious that it will work, because he's much more conscious of her than the other females around, given her usual clothes. After spending some time working to make him as horny as possible, she makes her move. One night, while Saber is out of the way and Shirou is too tired to be fully aware of what's going on, he wakes up to find a petite blonde with green eyes removing his clothes. If she's behaving differently from normal, he doesn't really notice. By morning, she's gone, and Saber acts as though nothing happened, but Shirou just assumes that was her being bashful. Mordred, meanwhile, is happy to have gotten Shirou, and smug about putting one over on Saber.
This continues for some time, with Saber none the wiser, as she and Shirou never have discussed sex outside the bedroom. But one night, when she was planning on sneaking into his room, she hears the sounds of Shirou clearly having sex. When she peeks in and listens more closely, she can tell that Shirou clearly thinks it's her in there with him, and Mordred's recent smug attitude suddenly makes a lot more sense. She considers confronting the issue right there, but the middle of the night is no time for arguments, and if she can resolve the situation without poor, dense Shirou ever finding out, so much the better in her mind. Unfortunately, while making that decision, her lover and child fucking in the next room turned her on, so Saber can't resist the urge to masturbate, right there in the hallway, watching Shirou and Mordred, continuing until they finish completely, too.
Saber confronts Mordred the next day, hoping to reason with her and put a stop to the whole thing. Mordred tells her that if she wants Shirou back so badly, she should take him back. But since Saber is trying to keep this secret from Shirou, violence isn't the answer. So she sets out to prove her superiority as a lover to Shirou. Except not. With a full week of effort, Saber couldn't get the same kind of response Mordred got the night she watched them together, owing largely to her own reserved nature. Mordred was willing and eager to go much further than Saber did.
One night, Mordred makes a special effort, pulling out all the stops to make sure that Shirou declares it by far the most satisfying sex he's ever had. Then she opens the door to Saber, in the hallway, masturbating and crying. Shirou suddenly clues in to the fact that he just fucked his "stepchild," and from her behavior, it wasn't anywhere near the first time. More disturbingly, he realizes that only that week of sex felt different from the last month/couple of months, and pieces together that he's actually been having a LOT of sex with Mordred. Way more than he's ever had with Saber.
The trio's respective issues lead them to a continual threesome. Saber is generally very passive, more having things done to her than with her. With Shirou and Mordred, they're more or less equally in it, fighting for dominance. I envision Mordred guiding Saber into a lot of things. Like Shirou walks in one night, only to find Saber with her ass cheeks spread wide and Mordred lubing her up for her first anal experience.
The alternate way I came up with for them to figure out what was going on was based on two simple thoughts. Those being, they wouldn't put Shirou in charge of birth control, and Mordred wouldn't bother finding out what it is. So when Saber comes to him, Shirou assumes she is good to go, and cums inside freely, thinking there's no problem. Until a couple months later, when someone notices Mordred is putting on some weight, is always sick in the mornings, and seems to be eating bizarre stuff. Imagine that stomach, in that top and shorts, bulging with pregnancy.