selfship!!!
for the sake of simplicity, i'm labelling this as a selfship, but to clarify; this is an oc x canon ship with an AU version of Shinji! (although all of my ocs have some elements of my actual self, so i see them all somewhat as self-inserts). the 'Atrophy AU' is my AU which begins before the events of Fate/Stay Night, follows the Unlimited Blade Works route, and changes some elements of Shinji's story.
My OC

Atro - It/They/She
An ageless entity whose existence is dedicated to exploring alternate timelines and universes, dancing between them as gracefully as a ballerina would, yet observing them with the clinical detachment of a scientist.
It can fit into any universe, and changes its appearance, age, and personality to fit into the world more smoothly, often fabricating a backstory to avoid revealing its true nature (though their personality often changes little, and they are usually seen as 'weird' and 'distant' by others).
They become easily fixated on specific events and characters, and may often insert themself into a world to see how events can be manipulated or characters can be influenced - often leading to the demise of that timeline, yet Atro is typically unbothered by this.
Atro takes up the role of a schoolgirl and becomes a childhood friend of Shinji Matou; while he protects her from being bullied for her 'weird' personality, she stays calm and collected when his temper gets the best of him, gradually teaching him how to handle his strong emotions better. Although Atro sees him more like a test subject than a friend at first, she does eventually develop feelings for him (though they're more akin to an obsession than normal love).
Atrophy AU
Atro and Shinji met at a young age, and became friends quickly after Shinji protected Atro from being bullied for its 'strange' personality.
Although initally confused by her neutral attitude towards almost everything, and her scientific way of seeing the world, he found their perspective interesting and began to feel protective towards them.
As they grow older together, Shinji's feelings begin to become more possessive of Atro, feeling jealous about its close friendship with Shirou and Sakura - he often acts on his jealousy, being passive-aggressive or demanding Atro's attention; it finds such behaviour fascinating rather than viewing it negatively, sometimes even finding it amusing.
Atro proposes the idea of their relationship becoming a romantic one, catching Shinji off-guard momentarily before he accepts their offer; although this changes little, with Atro remaining neutral and emotionally detached from most scenarios, and Shinji being possessive and clingy.
They do occasionally go on dates (usually Shinji's idea), and very slowly Atro begins to become more affectionate, curious about how Shinji will react - delighted at how flustered he becomes, she begins to develop genuine feelings for him beyond fascination, and becomes somewhat obsessive about him.
Though their mutual possessiveness concerns Shirou and Sakura, they are a positive influence on each other, with Atro fulfilling Shinji's desire to be special, and Shinji fulfilling Atro's desire to observe the complexity of human emotions.
Though the Fifth Holy Grail War still takes place and plays out the same as it does in the Unlimited Blade Works route, Shinji does everything he can not to involve or endanger Atro;
after his near-death experience, he leaves the pursuit of magecraft behind and plans his future with Atro, deciding to make use of his experience with computers to seek a career as a software developer.