Philip and Tom's relationship continues in the oscillating manner of their first meeting. At times they enjoy each other's company—Philip helps Tom with Latin and tells him extra-detailed war stories—at other times, Philip behaves "peevish[ly]" and bitterly about his deformity. Tom's education continues in the manner that Mr. Stelling sees fit, though much of it will be of no practical use to Tom in his profession.
Tom is happier in his second term with Mr. Stelling. Stelling does not push Tom so hard, now that Philip Wakem is around and academically accomplished enough to make Mr. Stelling's reputation respectable. Stelling has also hired a drillmaster for Tom—the local schoolmaster, Mr. Poulter. Tom enjoys Poulter's battle stories and begs him to bring his sword so Tom can see his sword exercises. Poulter, a man of questionable judgment who often drinks before his sessions with Tom, brings his sword one day and performs his sword exercises for Tom. Tom runs inside to get Philip, but Philip is in the middle of singing and yells at Tom for bursting in. They exchange harsh words, and Tom calls Philip's father a "rogue." Tom leaves the room and Philip cries "bitterly."
Back outside, Poulter agrees to let Tom keep his sword for the weekend in exchange for five shillings.
Maggie comes for a second visit to Mr. Stelling's. She notices Philip's cleverness and wants him to think her clever too. Maggie also has special feelings for deformed creatures because she finds them more grateful for her attention. Philip thinks Maggie seems nice and wishes that he had a sister.
Tom brings Maggie upstairs to show her his secret. When she is allowed to open her eyes, she sees Tom dressed as a pirate holding Poulter's sword. Maggie is gleeful at his costume. Tom unsheathes the sword and points it at her, intent upon inspiring respect and fear in her. Tom accidentally drops the sword while executing a cut and thrust, and it falls on his own foot. Maggie screams and tugs at Tom, who has gone unconscious. Mr. Stelling rushes into the room.
Tom has been seen by a doctor and lays in bed unable to walk. Tom fears he will be handicapped for life. Philip senses Tom's fear. He feels genuine dread on Tom's behalf and asks Mr. Stelling if Tom will be lame, reporting back to Tom the good news that he will soon walk well again. Tom invites Philip to come sit with him between lessons, and Philip accepts, spending much time with Tom and Maggie at Tom's bedside.
One day, Philip sits in the study with Philip while Tom's foot is dressed. Philip asks Maggie, "if you had had a brother like me, do you think you should have loved him as well as Tom?" Maggie replies, "yes," and admits that she would feel pity for Philip. Maggie soon senses her error in alluding to Philip's deformity and assures him she would admire his cleverness and talent and will never forget him. Philip tells Maggie that he likes her eyes, to her delight. Maggie kisses Philip and promises to kiss him when she sees him again.
When Mr. Tulliver comes to pick up Maggie, she reports how nice Philip is and entreats Tom to agree. Mr. Tulliver warns Tom not to try and be good to Philip, but not to get "too thick with him—he's got his father's blood in him." Tom and Philip never become close friends, and their personalities soon continue to be at odds.
Tom continued at Mr. Stelling's into a fifth session, at the age of sixteen, while Maggie went to a boarding school with Lucy Deane. Maggie hardly ever saw Philip again, and she sensed that he and Tom were no longer friends. Mr. Tulliver was now engaged in the lawsuit with Lawyer Wakem and Pivart, and any mention of the name Wakem angered him.
Tom continues monotonously with his education. He is now tall and pridefully reserved and is sure that his father's lawsuit will be decided in their favor soon.
One day in November, Maggie comes to the Stelling's to tell Tom that their father lost the lawsuit and is bankrupt. Tom is shocked, having foreseen nothing but perpetual success for himself and his father. Maggie further reveals that their father has fallen off his horse and has lost his senses. Tom explains to Mr. Stelling why he must return home, and Mrs. Stelling gives Maggie a basket of food. Tom and Maggie go "forth together into their new life of sorrow."
The introduction of the character Philip Wakem in Book Second begins one of the main conflicts of the novel. Maggie and Philip, sharing the same interests, grow fond of each other. Yet as Mr. Tulliver becomes more embroiled in his lawsuit against Mr. Pivart, as represented by Lawyer Wakem, Philip's name becomes less welcome in the Tulliver household. Philip's deformity—a hunchback—adds a subtler series of conflicts as some characters adjust their relationship with Philip according to their pity for him.
The depiction of Maggie in Book Second continues to stress her affiliation with animals. In Chapter II, we saw Maggie continue to shake her head, as though to shake her hair out of her eyes, even after her hair is pulled back. This action was described in Book First, Chapter II as "an action which gave her very much the air of a small Shetland pony." In Chapter V, Maggie's eyes remind Philip of "the stories about princesses being turned into animals." The references to Maggie's animalism point somewhat to her non-conformism—she doesn't use the artificial conventions of others, letting her natural exuberance dominate instead. Often, however, the references to Maggie's animalism coincide with some suggestion of magic or mythology, as in Philip's connection here and associations of Maggie with a "Pythoness" or "Medusa" in Book First.
Eliot continues to emphasize her own realism—few of her characters exist as blatantly good or bad and few of her situations are obvious and predetermined. Thus, she writes of Tom's response to Mr. Stelling's single-minded educational philosophy: "Nevertheless, there was a visible improvement in Tom under this training; perhaps because he was not a boy in the abstract, existing solely to illustrate the evils of a mistaken education, but a boy made of flesh and blood, with dispositions not entirely at the mercy of circumstances." Similarly, the interactions between both Tulliver children and Philip are portrayed as neither flatly antagonistic nor idealistically loving. Tom and Philip's relations, analyzed in detail, wobble in a gray zone of amiability. Maggie's like for Philip is not straightforward or ideal. In Chapter VI, she tells Philip that she would love him more for her pity if he were her brother. We also learn in Chapter V, that part of Maggie's affection for Philip hinges on her own need for appreciation: "Maggie had rather a tenderness for deformed things she was especially fond of petting objects that would think it very delightful to be petted by her."
Though Maggie and Philip enjoy a degree of mutual respect and interest, Maggie's relationship with Tom remains the focus of Book Second. Eliot continues to depict the two as a couple, though, by the end of Book Second with the jump in year between Chapter VI and Chapter VII, their childhood is over. Mr. Tulliver's bankruptcy and illness, along with Maggie's and Tom's reactions, will dominate the central part of The Mill on the Floss. Eliot uses biblical imagery of Adam and Eve's expulsion from Eden in the final image of Book Second, alluding to their newly fallen financial state, as well as the loss of innocence that accompanies tragedy and makes them into adults.