I really have problems with the idea of Twilight Sparkle as a mad experimenter willing to abuse unknown aliens just because they were unknown. Twilight has a lot of scientific curiosity, yes, but she also has a strong moral code, and Equestria is used to the concept of sapient non-equines. In several canon episodes she is willing to treat non-Ponies, non-Equines, and non-ungulates as "people."

I also don't think she'd be so easy to escape if she was a mad experimenter. She's an Alicorn, and I doubt that a random Human could kick her in the head hard enough to more than daze her a little, even if he caught her by surprise. Observe her fight with Tirek. Yes, she had the combined power of three other Alicorns as well as her own, but then the Narrator is far weaker than was Tirek during that fight.

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She's meant to be an antagonist for this story, so she is. That's basically how it goes. Sometimes it's Twilight. I don't see people complaining (except me) when writers make Celestia into the story's antagonist, which they do far, far too often. So Twilight-fans can handle it one of the few times it happens to be her.

Poor Twilight her Caring nature can sometimes be smothering she probably was was trying to study his biology to make sure he would survive the world he's in alien germs can be deathly harmful after all. but that's just my theory

@Jordan179 saying Twilight has a strong moral code, is rather stupid because have you forgot everytime she would freak out just like in lesson zero yes the other times were not as bad but she still had panic attacks when things you go bad also I think this story might have taken place before she became Alicorn because most of the fanfic that has Alicorn has her with her castle and this looks to be when the golden oak library was still there because anon had to stay in the basement