“guilty” was a separate stab between them.

Scout and Jem have a physical reaction to hearing Tom's guilt pronounced to the court. Because the evidence was solidly in his favor, they had not expected the jury to return such a verdict of injustice.

Jem doesn't even make it out of the courtroom before breaking down:

It was Jem’s turn to cry. His face was streaked with angry tears as we made our way through the cheerful crowd. “It ain’t right,” he muttered, all the way to the corner of the square where we found Atticus waiting.

This shows that Jem truly believed that his father's excellent defense was enough to convince anyone of sound mind that Tom could not possibly have committed the crimes he was accused of. However, at this point, the racist hearts of the jurors stand as a testament to the true power imbalance that exists in Maycomb—and Tom will suffer because of it.

Miss Maudie invites the children over for cake, and Jem reflects on these new understandings of racism:

I always thought Maycomb folks were the best folks in the world, least that’s what they seemed like.

Until now, Jem has existed in a fairly idealistic world, one where good always wins over evil. And this time, Jem has realized that sometimes evil people win the battle. He'd never seen the racist hearts alive in Maycomb until the conviction.

Jem begins to question the fairness of the entire legal system and tells Atticus,

No sir, they oughta do away with juries. He wasn’t guilty in the first place and they said he was.

Atticus tells Jem that it's not the legal system at fault—t's the faulty reasoning of men. At this time, a white man's word was going to trump a black man's every single time, regardless of facts. Atticus assures Jem that if twelve men with Jem's reasoning had been on that jury, Tom would have been cleared.

Jem begins to equate this sense of injustice of innocent creatures to the entire world around him. When a roly poly finds its way inside and Scout considers crushing it, Jem forbids it:

I lay on my stomach, reached down and poked him. He rolled up. Then, feeling safe, I suppose, he slowly unrolled. He traveled a few inches on his hundred legs and I touched him again. He rolled up. Feeling sleepy, I decided to end things. My hand was going down on him when Jem spoke.

Jem was scowling. It was probably a part of the stage he was going through, and I wished he would hurry up and get through it. He was certainly never cruel to animals, but I had never known his charity to embrace the insect world. “Why couldn’t I mash him?” I asked.

“Because they don’t bother you.”

Although Scout's understanding of the world is certainly changed after the trial, it is Jem who is more affected due to his being the older sibling and the one with a greater understanding of the complexity of all the verdict means. Forever changed, both children lose pieces of their childhood innocence following the trial.

The trial of Tom Robinson and the guilty verdict that he receives serves as another example of the loss of innocence that Jem and Scout suffer during the chapters of To Kill a Mockingbird. Before the trial begins, Scout has to deal with schoolmates and her cousin, Francis, who refer to Atticus as a "nigger-lover" for his defense of Tom. The children hear gossip about their father on the streets of Maycomb, and they see the support that Tom receives from the black community when they visit his church with Calpurnia. They see first-hand the anger and potential evil of the community when they come to Atticus' rescue from the lynch mob at the jail just before the trial begins.

Sneaking away to attend the trial in person, Scout and Jem witness the evidence presented and decide for themselves that Atticus has made a strong case for Tom's innocence. Yet the jury cannot overlook the fact that Tom is black and that Mayella is white, and they vote to convict him. Scout sees that the jury consisted of

... twelve good men and true... Then Mr. Underwood's meaning became clear. Atticus had used every tool available to free men to save Tom Robinson, but in the secret courts of men's hearts Atticus had no case. Tom was a dead man the minute Mayella Ewell opened her mouth and screamed.

The decision made Jem question the need for juries, and Miss Maudie had to respond to his "fatalistic noises," telling him that there were people in town who supported Atticus and how important he was to the community. Jem and Scout both feared for Atticus' safety after the threats made by Bob Ewell, and it made Jem recognize that there were distinctly different types of people living in Maycomb. Tom's death even made Jem more aware of the value of all living things, evidenced when he chastizes Scout after finding her about to "mash" a doodlebug. The outcome of the trial made both of the children grow up a little more quickly, once exposed to the real world where life isn't always fair and just.

Scout matures during the trial of Tom Robinson as she learns about violence and the dark side of humanity, as well as the complexity of human relationships and race relations in her community. She is still a child at the end of the novel, but she is a child with a deeper understanding of violence than most children her age. Though Scout may not have the sophisticated language to discuss her new knowledge, she does have more emotional intelligence, which makes her a dynamic character in the truest sense of the word.

At the start of the novel, Scout is getting into fights, hurting others physically, and recklessly acting on impulse before thinking through situations. Thanks to clear and respectful conversations with Atticus, who exposes Scout to the challenges of their experience in Maycomb rather than protecting her too much from suffering, Scout learns that her own tendency to violence isn't right. Physical violence in any form isn't acceptable, and when she and Jem are attacked by Bob Ewell on the night after the pageant, Scout gains a terrifying memory about physical violence no child should have to remember.

Scout develops more understanding of the trial process and empathy for the Ewell and Robinson families during the trial.

In the weeks and months leading up to the trial, Scout learns a lot about the legal process.  She does not really understand why her father is defending Tom Robinson, what Robinson is accused of, or why the residents of the town are reacting to her father with such disdain.  During the trial, she learns about the roles of race and class.

Scout follows the testimony well, and understands that Mayella had a tough life.

As Tom Robinson gave his testimony, it came to me that Mayella Ewell must have been the loneliest person in the world. She was even lonelier than Boo Radley, who had not been out of the house in twenty-five years. (ch 19)

This demonstrates an understanding of class and empathy.  Scout realizes that Mayella, as an Ewell, has certain disadvantages.

Scout also develops an understanding of race as she thinks about Tom Robinson’s life, and the people’s reactions to him.  For example, when Tom says he felt sorry for Mayella, Scout realizes that this is a fatal mistake.

The witness realized his mistake and shifted uncomfortably in the chair. But the damage was done. Below us, nobody liked Tom Robinson's answer. (ch 19)

One could argue that the Tom Robinson trial did not have a profound effect on the prejudiced culture of Maycomb and the town remained ignorant, intolerant, and racist to its core before, during, and after the trial. However, tensions did rise throughout the community as many citizens criticized Atticus for defending a black man and publicly ridiculed his children. Scout and Jem certainly had to deal with the community's backlash regarding their father's decision to defend Tom, and Atticus had to risk his life saving Tom Robinson from a lynch mob on the night before the trial. On the day of the trial, people traveled for miles to witness the spectacle and the community's attention was directed towards the courthouse.

Atticus understood his racist community and did not expect to win the case, which is why he was not surprised by the verdict. Despite the fact that Tom Robinson became a victim of racial injustice, Miss Maudie believes that the community of Maycomb made a small step towards equality. She acknowledges Atticus's efforts and also tells the children that Judge Taylor supported Tom as well as Sheriff Tate and the entire black community. Following Tom's death, Scout mentions,

"Maycomb was interested by the news of Tom’s death for perhaps two days . . . To Maycomb, Tom’s death was typical. Typical of a nigger to cut and run. Typical of a nigger’s mentality to have no plan, no thought for the future, just run blind first chance he saw. Funny thing, Atticus Finch might’ve got him off scot free, but wait—? Hell no. You know how they are. Easy come, easy go. Just shows you, that Robinson boy was legally married, they say he kept himself clean, went to church and all that, but when it comes down to the line the veneer’s mighty thin. Nigger always comes out in ‘em" (Lee, 128).

Scout's comments reveal that the community of Maycomb remained a racist society, where black people are discriminated against and viewed as second-class citizens. Overall, one could argue that the Tom Robinson trial brought excitement to the town of Maycomb but did not inherently change its racist culture.

This question assumes too much.  It assumes that the trial changed the town.  It would be great if Lee wrote about how the injustices and the racism of the town caused an uproar and changed ensued.  Nothing like this happened.  The sad thing about the novel is that nothing changed.  Racism is still alive and well.  We can see this is two pointed situations. 

First, when the Women's Missionary Society meet, we can see that nothing has changed.  They do not speak of the miscarriage of justice in the case of Tom Robinson.  Instead, the women say that the blacks are more emboldened by Tom Robinson to misbehave! So, rather than seeing the injustice, the women of the Missionary Society only complain. 

Second, we see blindness in the schools. Miss Gates is the perfect example. She chastises the racism of Hitler, but she does not see the racism in her own town.  She is completely sanctimonious. Her words say it all:

“Very good, Jean Louise, very good,” Miss Gates smiled. In front of DEMOCRACY, she printed WE ARE A. “Now class, say it all together, ‘We are a democracy.’”

Atticus Finch opens Scout's mind and heart to what secrets lie in human nature.

In the evenings, Atticus holds Scout on his lap, where she has learned to read the Mobile Register with him at night. As she sits with her father, Scout feels secure and content. She even gains some confidence from her reading about adult matters.

When Jem and Dill try to communicate with the ghostly Boo Radley, Atticus scolds them and impresses upon them that they must leave Boo alone and respect people's privacy. Similarly, Atticus teaches Scout and her brother to be respectful of those who struggle secretly against private demons, such as Mrs. Dubose. By revealing the pain Mrs. Dubose has endured, Atticus teaches Scout to perceive her as a woman who is suffering so that she can die without regrets, tied to nothing, and with some dignity. After she dies, Atticus says,

I wanted you to see what real courage is . . . . It's when you're licked before you begin but you begin anyway and you see it through no matter what.

Further, by means of his own conduct, Atticus directs Scout to have integrity and to be modest about her own talents, as he is about his excellent marksmanship. After her confrontations with Cecil and her cousin Francis, Atticus teaches Scout to be patient with people so that they will, hopefully, become comfortable enough to be honest about their feelings. Above all, Atticus demonstrates to Scout the high value of integrity and the respect one must have for the human value and rights of everyone, no matter one's social status or color. 

There are a few factors that account for the change in the relationship between Jem and Scout. As they get older, they slide into more adult roles of male and female. Since Maycomb is a town where race and gender roles are quite clearly marked, roles which sustain a tradition that comes with racist and stereotypical practices byt the way, the older Scout and Jem get the more they are likely to fall into these roles. Thankfully, Atticus teaches them that roles can serve a purpose but such notions should be abandoned if they are used to sustain a culture of racism or exclusion. Young as they are, the children do not change their relationship because of Maycomb's class system; it just bears mentioning here.

The main reason the relationship changes is because Jem is a bit older than Scout and he's going through all the identity issues of an adolescent. It's also quite clear that he embraces growing up and Scout does not. Scout feels pressured into becoming a lady and feels awkward wearing a dress during Aunt Alexandra's missionary meeting. But Jem struggles forward to his teenage years. In Part Two, which begins with Chapter 12, Scout notes Jem's changes:

Overnight, it seemed, Jem had acquired an alien set of values and was trying to impose them on me: several times he went so far as to tell me what to do. After one altercation when Jem hollered, “It’s time you started bein‘ a girl and acting right!” I burst into tears and fled to Calpurnia.

Although Scout is quite curious and intelligent, Jem, being the older sibling, understands things a bit better. When Tom Robinson is convicted, it is Jem who is more upset because he's beginning to see the hypocrisy of the adult world.

Another reason the relationship changes is that their routines change. In Chapter 26, Jem enters seventh grade and is in the high school. He also goes out for football and doesn't get home until late. When they were younger, Scout and Jem simply spent a lot more time together. At the end of the chapter, noticing Jem became upset at the mere mention of the courthouse and trial, Scout went to Atticus for advice.

Atticus said that Jem was trying hard to forget something, but what he was really doing was storing it away for a while, until enough time passed. Then he would be able to think about it and sort things out. When he was able to think about it, Jem would be himself again.

This is Atticus' way of telling Scout about growing up. Going through adolescence, Jem is still the boy Scout grew up with but he's attempting to fit in. High school is like Maycomb in a sense. There are expected roles, classes, and cliques already established and kids usually find it easier associate with one of these groups. Jem is no different except that, from Atticus' teaching, he has a subtle indication that these expectations to fit in, just as they exist in Maycomb, can be used for opposing reasons: to allow people in and to exclude others. This might not be in the front of Jem's mind but it bears mentioning again. More than anything else, Jem embraces adulthood and even though Scout is a sponge for knowledge, she withdraws from adulthood (well, lady-hood is more like it).

After the trial of Tom Robinson and his unjust conviction, the naivete of Jem is lost, and the innocence of Scout is certainly diminished as is that of Dill.  In Chapter 22, at the trial's end, Jem finds himself in tears, as Dill has been earlier when Mr. Raymond says of him,

"Things haven't caught up with that one's instinct yet. Let him get a little older and he won't get sick and cry. Maybe things'll strike him as being--not quite right, say, but he won't cry, ot when he get a few years on him."

Indeed, things are "not quite right" for Jem, who mutters on the way home, "It ain't right"; later, with great indignation, he asks his father, "How could they do it, how could they?" Clearly, Jem is disillusioned. He reflects,

"I always thought Maycomb folks were the best folks in the world, least, that's what they seemed like."

And, Dill becomes cynical; he declares that he is going to be a clown when I grows up:

"There ain't one thing in this world I can do about folks except laugh, so I'm gonna join the circus and laugh my head off."

Once the children are home, Atticus talks to Jem, explaining how the society is set up, an arrangement that causes reasonable men to "lose their heads." He also explains how there was some consternation in one man's mind, a fact that gives Atticus hope.

After talking with his father, Jem attains some maturity, as does Scout who listens. Certainly, Jem's faith is people is shaken, but the words of Miss Maudie about the integrity of his father encourage Jem and his sister. Truly, it is a much more mature Jem and Scout who now understand the weakness and foibles of human nature. 

Atticus is disappointed when Tom Robinson is convicted and then kills himself trying to escape prison.  He knew that he was never going to win the case, but it affects him just the same.  Although Atticus explains to his children that the case is almost unwinnable, he also tried his best and really tried to make a difference for Maycomb.  

Atticus realized that acquitting Tom Robinson, despite the lack of evidence, would be very hard for the jury.  He still tried to explain to them why they should.  He may have given one of the most important closing statements of his career. 

Atticus explained to the jury that there are good men and bad men, regardless of race.  He reminded them that there was no evidence to prove that a crime even took place, and he had proved that Mayella’s injuries could not have come from Tom.  He also showed what Mayella’s home life was like, and how her father most likely was the one who beat her up. 

“…A court is only as sound as its jury, and a jury is only as sound as the men who make it up. I am confident that you gentlemen will review without passion the evidence you have heard, come to a decision, and restore this defendant to his family. In the name of God, do your duty.” (Ch. 20) 

Atticus earned the respect of the black community, and also that of others who felt that racism had seen its day.  The case took its toll on his family though.  Although Atticus did not take Bob Ewell’s threat seriously, his children were scared.  The ultimate effect was when Ewell attacked his children, injuring Jem and possibly doing worse if Boo Radley had not intervened. 

By this time, Atticus is clearly worn down.  He thinks about the impact it will have on Jem, but Heck Tate decides that they should say that Bob Ewell fell on his knife.  This prevents either Jem or Boo Radley from taking responsibility. 

“I’m not a very good man, sir, but I am sheriff of Maycomb County. … Know everything that’s happened here since before I was born. There’s a black boy dead for no reason, and the man responsible for it’s dead. Let the dead bury the dead this time, Mr. Finch. Let the dead bury the dead.” (Ch. 30) 

Atticus thanks Boo Radley for saving his children.  Scout walks Boo home, and reflects on the events of her childhood.  The events of the book are Scout’s story, but they are also Atticus’s.

During the trial Mayella testifies to her rape by Robinson.  When Atticus begins his cross-examination he is very calm, deliberate and polite.  He tells her he wants to "get to know" her.  As he progresses in in cross, he becomes more aggressive and even though he is still polite and compassionate, he is trying to break her down enough to tell the court that her father is the one who beat her.  The cross can be found around pages 194-200 in my edition, chapter 18.

The first noticeable change in the relationship between Jem and Scout is at the beginning of Chapter 2 when Scout attends school for the first time. Prior to this, Jem and Scout were often together when Jem was home. But on the way to school, Jem explained that since he was in fifth grade and she was in first, he did not want her to hang around him at recess or embarrass him in any way. This was Jem just protecting his school image from that of his private life at home but he also wanted to show Scout that fifth graders did not hang out with first graders. This kind of hierarchy is interesting because it is similar to how the children learn of Maycomb's class system in which the closed-minded population of Maycomb believed in setting social boundaries between white and black, and between poor and rich. 

In Chapter 12 (the beginning of Part Two), Scout notes that Jem has been difficult. This is following Mrs. Dubose's death. Jem is twelve at this point and he's becoming an adolescent/young man. Scout narrates: 

Overnight, it seemed, Jem had acquired an alien set of values and was trying to impose them on me: several times he went so far as to tell me what to do. After one altercation when Jem hollered, “It’s time you started bein‘ a girl and acting right!” I burst into tears and fled to Calpurnia.

Calpurnia explains to Scout that Jem is simply growing up. He's becoming more interested in how a boy/man is supposed to behave. And since he's getting older, he is starting to think more like an older brother than a playmate to Scout. Many of the changes in the relationship between Jem and Scout have to do with Jem's development and maturation. Their relationship changes again (Chapter 26) when Jem starts going to the high school, seventh grade, and Scout sees him less and less.