.
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When he was alive, Rin used to tease Shirou that he was the girl in the relationship.
It made sense: he was the one who cooked, who cleaned, who worried about her when she came home too late. Even when he left the clock tower and roamed the desert with the other mercenaries, he still worried over Rin's beddings and was the one who procured their food (it was comical, actually. Seeing Shirou, broad-shouldered and wearing camoflaged fatigues, bending over a little hotplate on the counter and warming up a can of stew, tasting and stirring it as if he had actually made it.)
The other thing was, Shirou was really passive in bed.
Not that he couldn't be passionate - Shirou knew how to work Rin into a frenzy, if Rin asked him to - but she knew what he liked best was slow and gentle, that he liked it when she climbed on top and took him with slow, deliberate strokes. He would close his eyes and lay his head to the side, like a damsel in a romance novel, panting softly with a blush on his cheeks. When he would come, he would reach a mute state of pliable senselessness, eyes closed like half-moons while his mouth would open in a soft, silent 'o.'
Archer doesn't seem to be aware of it, but unless Rin specifically asks, making love to him is exactly like making love to Shirou.
Of course, Rin knows they are the same person. Shirou at his core hasn't changed, even if he's become somewhat hardened by his experience as a guardian, and while Shirou-as-Archer is more sarcastic and more prone to excessive eye-rolling, in bed he craves the same sort of comfort. When he's on top he likes to kiss her slow and deep and rest his face in the crook of her shoulder, and when she climbs up on top of him, his eyes will close into those same two half-moons, his face will crack into a blush, and he will look every bit as helpless to her ministrations as a damsel in a romance novel.
So she calls him "Archer," to goad him. Be more aggressive, throw her on the bed. Rip off her clothes, like she wants him to, and Shirou obliges because he never says no. (Rin would never force him if it made him uncomfortable. And she knows him well enough to tell when she's overstepped her bounds, when he's doing something that makes him uneasy and embarrassed. Any other lover would take advantage, but not Rin. Rin knows how to take care of him.)
Tonight, she can tell that Shirou doesn't want to be aggressive. He appears in front of her, drenched in moonlight, looking weary and fatigued and in desperate need of comfort. So she kisses him gently and pulls him into bed. Makes love to him by climbing on top, touches him and caresses him, watches that blush crack across his face. He is as tender and helpless as a child, it seems, and when he comes, it's with a silent shudder, pulsing inside her with a breathy moan.
She lays on top of him and listens to his heartbeat, dropping soft kisses along the line of his jaw and his collarbone, and waits for one of them to decide when to get up and clean themselves off. She decides he'd better be the one, because he seems comfortable and awfully close to falling asleep, but also because she doesn't want to risk hurting his feelings.
And Shirou does eventually get up, moving out from under her with difficulty and grimacing a little at the large wet spot in the middle of the bed. They shower and dress and she helps him tug off the bedclothes and pull on a fresh sheet over the mattress. Then they sink against each other, Rin cuddling him and kissing him and making him feel safe.
She doesn't mind doing it like this, sometimes. But personally she'd rather just call him "Archer."