Tom goes to school under Mr. Stelling for his first term. The experience is jolting to Tom—he is Mr. Stelling's only student and feels inadequate to the Latin and Euclid that Stelling attempts to teach him. Mr. Stelling, who considers Latin and Euclid the only measurements of intelligence and only methods of teaching, scolds Tom for his supposed laziness. Tom becomes "more like a girl than he had ever been in his life" as both his pride and sense of correctness in his previous way of life are diminished. He feels lonely—his only distraction being Mr. Selling's toddler, Laura—and he wishes for Maggie's presence.
Maggie comes for a visit before the end of term. Maggie condescendingly offers to help Tom with his studies and sits to study his Latin and Euclid, both of which take her longer to understand than she supposed. She impresses Mr. Stelling with her intelligent chatter but feels mortified by his allusion to her attempt to run away to the gypsies, and his comment that women have only "superficial cleverness" and are "quick and shallow." Tom is sad when Maggie leaves.
Tom goes home gratefully for Christmas at the end of the half-year, happy to see his familiar home. The narrator meditates upon one's affection for the worn furniture of childhood versus the impulse to acquire newer, nicer things.
Christmas at the Tullivers' is tense, as Mr. Tulliver is preoccupied with the problem of Mr. Pivart, a new landowner upriver who purports to use some of Mr. Tulliver's waterpower. Mr. Tulliver suspects that Lawyer Wakem supports Pivart and would represent him in future litigation. Mr. and Mrs. Moss are supportive of Tulliver at Christmas dinner, but Mrs. Tulliver begs him not to "go to law" and laments his stubbornness. Mr. Tulliver's lawyer, Gore, is less clever than Wakem, yet Mr. Tulliver is likely to go to law against Wakem, as he still bears a grudge over a suit that Wakem won against him, costing Tulliver his private right of road and the bridge. Additionally, Mr. Tulliver is goaded by the fact that he has been forced to borrow money from Wakem's office to repay Mrs. Glegg.
Tom has learned that Wakem's son will be sent to Mr. Stelling next term. Mr. Tulliver warns Tom not to be antagonistic toward Wakem's son despite his own grudge against Wakem, as the boy is a "poor deformed creatur."
Tom arrives back for his second half-year at school with Mr. Stelling, and a new student has arrived—Philip Wakem. Tom and Philip have their first meeting, and both boys are wary of each other—Tom because he knows Philip's father to be a bad man; Philip because he is afraid of being jeered at for his humpback. The ice is soon broken when Tom notices Philip's talent for drawing, and the conversation moves easier. Then Tom spontaneously asks Philip if he loves his father, and Philip defensively replies "yes." Tom is quite sure of his own father's righteousness, as well as the fact that Lawyer Wakem is evil, and his son must be bad, too, if he loves his father.
Philip and Tom are not to have the same lessons because Philip is much more advanced and intelligent. The boys reconcile through Philip's knowledge of Greek war stories. Tom then tries to reassert his superiority in the face of Philip's older age and knowledge of fighting stories, by indirectly reminding Philip of his handicap.
If most of Book First focused on Maggie, Book Second concentrates fully on Tom's school years at the house of Mr. Stelling. In the same ways that Maggie has suffered in her childhood with an external world that is much at odds with her personality, Tom suffers in the unfamiliar environment of higher education. Eliot seems to invite this connection and stress gender for the first time, when she repeatedly mentions that Tom is now "like a girl." Here, being a girl refers to a state of being in which external pressure has colluded to make one feel weak. It is only in subtle points such as this that Eliot indirectly calls attention to the fact that part of the difficulty Maggie feels in simply existing comes from her gender. Indeed, we see in Chapter I that even Mr. Stelling, who values education and intelligence, holds generalized ideas about female capabilities—women have "a great deal of superficial cleverness; but they couldn't go far into anything." Mr. Stelling, like authority figures in Maggie's life, also does not consider the effect his statement of this judgment will have on Maggie.
Tom's difficulty in coming to terms with Mr. Stelling's idea of education and general value systems is also mirrored in Mr. Tulliver's bafflement in relation to potential litigation over waterpower from the Floss in Chapter II. Both Tom and Mr. Tulliver are depicted as characters who imagine physical solutions to social problems. Tom brings percussion caps to school to help him fit in and be respected. In Chapter II, Mr. Tulliver imagines the law in terms of a cockfight, "it was the business of injured honesty to get a game bird with the best pluck and the strongest spurs." Both Tom and Mr. Tulliver seem baffled, to an extent, by intricate, slippery language. Tom does not understand Mr. Stelling's educated humor about declining his dinner or a Latin verb, and we have already seen Mr. Tulliver's early judgment in Book First, Chapter II, "it's puzzling work, talking is." Both face up-and-coming adversaries—Mr. Stelling and Mr. Pivart are not from established, local, provincial families like the Tullivers but instead have arrived recently on the scene and intend to make money quickly. This ethos of rapid wealth rests on speculation and on qualities that seem vague to the Tulliver men. Mr. Stelling would rise in the world based on his investment in others' perception of him as a learned man. Mr. Pivart would rise in the world based on the deceptive intricacies of litigation and invisible waterpower. Tom and Mr. Tulliver do not have heads for these sophisticated ways of money and image making, so foreign to their own ethos of cumulative saving. Mr. Tulliver remarks in Chapter II of Mr. Pivart's claims to water power: it's "a very particular thing—you can't pick it up with a pitchfork." This clash between the Tulliver's older, provincial way of life and the newer aggressive materialism is presented neatly in the narrator's meditation at the end of Chapter I on the affection for the weathered furniture of one's childhood versus the impulse to acquire newer and better housewares. The narrator warns of the dangers of unchecked materialism—"who knows where that striving might lead us"—and speaks of the important affection for tradition.