In "Eli Whitney's Flesh-Eating Mistake," she is seen outside of her orphanage, titled "Sister Thornly's School for Wayward Tots." She is seen filing her nails and counting the orphans playing outside, ignoring their roughhousing. When she realizes that she is one orphan short, she realizes Otto is not outside and goes inside, listening carefully. In this way, she hears him turn a page in his book while he secretly reads in a closet by a flashlight. She catches him, and punishes him for reading. When Otto is finished with his chores and is visited by Tuddrussel and Larry in his room, Sister Thornly hears noises and knocks on Otto's door, warning him about "reading racket." Otto manages to get rid of her by assuring her he was mending his toilet scrubber rack.
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This article contains plot details about a later episode.
In "Orphan Substitute," Otto shares some of his orphanage memories with Larry, including many field trips. While the field trips were labeled for visiting national monuments, Sister Thornly really was taking the kids near the sites and having them work for money. In the episode, the Time Squad is called to Washington DC in 2002, while Sister Thornly happens to have the orphans taking government surplus cheese near the capitol. Otto wanders from Time Squad and is taking pictures of the US Mint when Sister Thornly hears him and throws him on the bus, back to the orphanage. At the orphanage, Sister Thornly has Otto doing chores again, but it's not clear whether they are a punishment for leaving, or simply because she dislikes him. When Otto leaves and a spelling bee champion orphan is left, Sister Thornly accepts it, saying one orphan genius is as good as another.
Sister Thornly is a large, elderly woman. However, she is strong, and is not bothered by dragging kids around. She is dressed in a nun's "habit," and wears a gold whistle around her neck, though she is never seen using it. Her eyebrows are large black rectangles over her eyes, and she has a long, slightly pointed nose.
She is incredibly hateful towards children, especially towards Otto, whom she prohibited from reading, which is his only enjoyable pastime. In "Eli Whitney's Flesh-Eating Mistake," while she is outside with the other orphans, she doesn't bother to stop their roughhousing, showing she doesn't care when they get hurt. In "Orphan Substitute," she is impatient at the children who are throwing cheese onto the bus, not allowing them to take a break and warning them that this is the only food they will get. The orphans in that episode are dressed poorly as well, showing that they are poorly cared for. Interestingly, even though Sister Thornly hates Otto, she never mentions his absence from the orphanage when she finds him again. This could show that she may not have even noticed his absence.