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Scully is different, and so immediately endearing to Mulder, because she’s the first person to want to know what he thinks, and why he thinks the way he does, instead of writing him off outright. He's an interesting puzzle to her. Even if she’s steadfast in her constant disagreement, her curiosity itself is—in a way—an act of validation, respect, care.

Mulder is so immediately endearing to Scully because the way he thinks is unusual for their profession, and probably refreshing. He's anti-bureaucratic, emotionally sensitive, unapologetically strange. A "lone wolf" yet so open and easily taken by her. It turns out, his curiosity in the supernatural was born from something equally fascinating, and all too rare: his care for other people.

Mulder, totally agreeing: "Oh, she's not usually like that. Usually, she's rigid in a way that one might actually find quite charming, as I so often do!"

Random character: "Your partner is a complete nutcase."