Shinji is very protective of his sister, Sakura.

More possessive than protective.

Matou Shinji [Person]
Source: Fate/side material (2004-1-30), p.074
Fate Dictionary
Shirou's friend. Sakura's older brother.
As Rider's Master, Shirou comes into conflict with him on numerous occasions.
Though he is selfish and has the bad habit of looking down on other people, he is virtuous in his own way, and while he may be warped he is not actually a bad person.
He values rules (but he doesn't follow them himself), he hates injustice (if he's not the one responsible), and he is kind to women (excepting "his" women, of course). As you can see, he's clearly a pretty cool guy.
Due to the gap between his "ideal world" and the world he actually lives in, his personality has become warped, but when Shirou first made his acquaintance four years ago he wasn't nearly as bad as he is now.
As you might expect, he stumbled across Shirou doing menial tasks for people free of charge, and despite (seriously) deriding him as an idiot from behind his back, he hung around with him until he was done. At the end of the day, Shinji laughed as if he was having a good time, and exclaimed, "You may be an idiot, but you sure do good work, at least!"

>>161324480
(cont.)

Perhaps Shirou appreciated Shinji's honesty despite his foul mouth, because afterward they became friends.
Though Shinji often made fun of him, in the shadows he socially assassinated anybody that took advantage of Shirou, and frequently invited him over to his house to hang out. It seems they really were close.
However, as you know, for a temperamental genius like Shinji even a friend of many years is not safe from suddenly becoming his enemy for incomprehensible reasons.
Basically, he's the kind of person that's reliable when he's on your side but ends up being really troublesome if he turns on you.
Originally there was going to be an option to accept his invitation to join forces in the Saber route, but tragically we ran out of time and were forced to cut it.
Ah, if we'd included that route (let's call it the "Shinji route"), players would have gotten to see a bit of Shinji's good side, but there was just no way. Please, find it in your hearts to forgive us!

>>161324480
>>161324522
Shinji seems pretty cool (for a douche) from this description, but Nasu had trouble with actually conveying this and thus making sense of Shirou and Sakura's relations with him.