This was written like a million years ago (2008 maybe). I always loved this pairing and I wanted them so badly to be together in the end (somehow I like dark Stein). I'm bringing it back to life because I just re-read the manga and felt like it. Enjoy!
Disclaimer: Soul Eater belongs to Atsushi Ohkubo, not me.
It was a black, non-starry night. It was all in the dark, immersed in gloom. But not enough for him not being capable to see her silhouette in the sky, outlined on the dim light of the waning moon.
She, a woman as dark as that night, riding her flying broom and smiling as a wicked witch from a tale. However, she was a witch much worse than the ones that filled the children's nightmares. Her smile was horrible and treacherous. It invited him to join her, to stop trusting and believing in his cause. It offered him the possibility of plotting maleficent plans, of exploring the most terrible secrets inside him. Those ones that he suppressed deep down but he actually wished to release.
Stein knew that smile was for him. He knew that she'd wait, she'd wait while she lived, no matter if in her human form or under the appearance of thousands of snakes. She'd do everything and more to force him to abandon and surrender her. She'd brutally increase his madness till he had no sanity anymore and then he'd be unconscious, deranged, confused. So he'd come crawling, begging for some corpses to dissect and asking her for teaching him till he satisfied his thirst for knowledge.
That was the reason why Stein knew, even if he didn't admit it, he was inevitably lost. He'd always been. Because she loved him back then and despite of everything she still loved him. The witch wanted the mad Stein in order to possess his knowledge and rule the world along with Kishin, no one overshadowing them. But Medusa-sensei, the nurse, wanted Stein for them to feel a bit more human despite their respective inner darkness. She wanted them to be a little closer from the good she never left completely because she was somehow tied to the professor.
That was how Stein learnt he hadn't kill her when he pierced her with his scythe. Even if the little sane conscious that he still had left yelled him the opposite thing to convince himself.
Stein knew many, too many things. Some of them he'd prefer not knowing. But what remained in his soul with overwhelming certainty was the fact that he could love, too. Despite his unstable personality, he loved the wrong woman. So he knew that these feelings living in the deepest place of him one day would be his downfall.