An extended summary of Kafka on the Shore (a magical realism novel wherein we find the main character with an Oedipus complex) in three parts. You can find part 2 here.

Kafka in another world
The second time at the cabin, full of thoughts, and alone, Kafka goes into the forest. He calculates, it is Tuesday at 2 pm, the day and time Miss Saeki gives a tour of the library (On this day, she is, in fact, giving a tour to Mr. Nakata and Hoshino). In the forest, Kafka goes beyond the familiar. He ventures deeper into the forest on a barely discernible path, but gripped by fear of getting lost, he turns back. That night in the cabin, Kafka, in a dream, forces himself on Sakura by invading her dream. His presence and sex with her is unwelcome on Sakura’s part. Even if they are not blood related, they are definitely brother and sister, she tells him.
For Kafka, it is all part of the program and the curse; he aims to fulfill it. He is tired of being in someone else’s schemes; he is going to make the scheme his own.
The following day, Kafka goes back into the forest with tools he will need to make it—sharpened hatchet, compass, spray paint to mark his way, emergency food, canteen etc. In the forest, Kafka and Crow talk. They realize that although Kafka has killed his father, violated his mother and his sister, the curse is still upon him, it’s branded on his very soul and DNA. His confusion, fear, anger, unease are still inside, torturing him. He struggles with his identity; feels lost. He doesn’t know what makes him who he is. He considers wiping out his “me” right there , and so end his battle with his consciousness; letting his DNA rot among the weeds.
We see Kafka transforming; getting rewired. He throws away his security, the tools he brought with him—sharp hatchet, rucksack and all; defenseless, he forges on. He takes only his fathers hunting knife in case he needs to slash his wrists. He feels a hollow man, a nothing man, a void, therefore with nothing left to fear. The forest and all the fears it holds for him are part of him, this journey is taking place inside him. He struggles with the question whether his mother did not love him? The question has tormented him for years. Why would Miss Saeki (his theoretical mother) abandon him?
Crow tells Kafka that his mother abandoned him because of fear and anger such as he has. But he must forgive her or else he will become her. Still young, he can live a different life.
Advancing and still struggling within himself, Kafka meets two long lost Japanese soldiers dressed in the old imperial army fatigues. They are waiting for him. They identify themselves as the two soldiers disappeared in the forest during World War II. The soldiers, one a farmer and the other a recent college graduate at the time, didn’t want to kill or be killed in war. Rather than go fight in war, they simply walked away during training.
The soldiers are now in a place, an alternate world, where there is no difference between a long long time ago and now. Here, time does not matter. The soldiers stand at the entrance to this alternate world. When Kafka gets there, the entrance is open. Without knowing the ultimate purpose, Mr. Nakata opened the entrance for Kafka.
The soldiers tell him whether he enters or not is up to him, but if he stays in this other world long, he may not get back to his normal world. Kafka chooses to enter—there is someone he must see in this other world.
The soldiers and Kafka start to walk; it is a brisk pace for Kafka, he struggles but keeps up. He is the toughest 15 year old. To calm his fears, the soldiers tell him the forest wishes him no harm. Climbing over a hill, the soldiers show Kafka the place he is to enter. There are a couple of roads and a few buildings. There can’t be that many people living there. The soldiers take Kafka to a dwelling that looks like Oshima’s cabin. It is the same shape and size; the difference is in the furnishing that include a TV.
Kafka turns on the TV; the Sound of Music is playing. The girl, the 15 year older Miss Saeki who visited him at night in his room at Komura Library is here in this other world wearing the same clothes as in the library. More real than a dream. She cooks Kafka a meal; she will be cooking, washing and cleaning for Kafka, but she has no name—they don’t have names in this other world. Kafka tells her he came to meet her one more time. She tells him time doesn’t matter here, memory doesn't matter here.
The grown Miss Saeki meets Kafka in this other world too. She will not remember many things for long, including her time with Kafka. She tells him to get out of this other world before the entrance closes. It will close soon. He protests. There is no back there for him, no one to love or care for him. But she insists, and wants Kafka to go back so he can remember her. And she wants Kafka to take the painting of her long time dead lover from the room in the library and keep it with him wherever he is. He was there a long time ago, and when Kafka closes his eyes, he remembers that he was there. She sat beside the painter and was in love with Kafka. Miss Saeki regrets leaving and losing Kafka. She asks Kafka for forgiveness and he forgives her. His frozen heart dissolves.
Kafka heeds Miss Saeki’s words and leaves this other world. The soldiers wait, ready to lead him out of their world to the entrance. He betrays no regret for leaving and going back to his own world.
Johnny Walker in purgatory
While Kafka is in this other world, the boy named Crow manifests and meets Johnny Walker. Johnny Walker is sitting on a rock in a forest clearing. Crow flies in from the ether to perch on a branch nearby. The man realizes Crow does not want to talk, but the man talks away. He tells Crow that he has flutes in his bag made from the souls of cats, but he has made enough flutes. He is not going to make any more. The man is heading where he can turn all the flutes into a single, more powerful flute. He also tells Crow he is in limbo; a neutral point and gloomy place between life and death. He is the slug-like thing that does not make it into the entrance when Hoshino closes it.
And Johnny Walker also boasts to Crow that Crow can’t harm him—this is Kafka realizing he needs to move on from his estranged feelings for his now dead father.
Closing the entrance
With the entrance open, and Mr. Nakata fast asleep as is his wont, Hoshino asks Sanders what to do. Sanders says to keep the entrance open till it must be closed. He also tells Hoshino that they move to an apartment he has prepared for them; the police are after them. At the apartment, Mr. Nakata informs Hoshino that he killed Johnny Walker. However, he will not surrender himself to the police; there are things he must finish—he needs to close the entrance, then he will be normal again. Hoshino wonders whether there is a connection between Sanders and Johnny Walker, he only gets more confused. Better leave it alone, “Pointless thinking is worse than no thinking at all.”
When Hoshino and Mr. Nakata opened the entrance stone, they knew something happened somewhere, though they did not know what (It was the entrance and egress by Kafka in and out of the alternate world, and the inalterable and final entrance into the alternate world by Miss Saeki).
Mr. Nakata asks that they find a car and drive around the city looking for something. Mr. Nakata does not know what; he will know when he sees it. They search for two days. On a day when Hoshino takes a wrong turn on their way home, Mr. Nakata sees the Komura Library. It comes to him that it is what they are looking for. But it is closed. They go back the following day.
At 2 pm Miss Saeki gives Hoshino and Nakata a library tour. At the end of the tour, Mr. Nakata, pursued by Oshima and Hoshino, forces his way upstairs back into Miss Saeki’s office. He wants to talk about the entrance stone. “I think I have been waiting for you,” she tells Mr. Nakata. His arrival is perfectly timed. Any sooner or later, she would not have known what to do. Miss Saeki knew about the entrance stone. She came across it, and opened it a long time ago to preserve her perfect relationship with her lover. Her opening the entrance stone set off the events that happen to the people in the novel. Her unhappy life was her punishment for opening it.
Mr. Nakata re-opens the entrance to restore things the way they should be. He explains to Miss Saeki that he killed Johnny Walker, in of place of a 15-year old who should have been there. He also tells Miss Saeki that she can’t stay in this world anymore.
That same afternoon, Oshima finds Miss Saeki dead in her office. She enters the alternate world never to return.
The following day, Mr. Nakata too dies in his sleep; the entrance is yet to be closed. Alone, bored and not sure what to do in the apartment with a dead body, Hoshino narrates his life to the entrance stone. He realizes how pointless his life had been. He also realizes he is now able to talk to cats—he has now taken Mr. Nakata’s role. A cat outside the apartment tells him he has to kill it, and that he will know it when he sees it. He must kill it for Mr. Nakata. The thing to be killed crawls out of the dead Mr. Nakata’s mouth. It is as thick as a man’s arm, and about a yard long and looks like a slug. It glistens like mucus. It used Mr. Nakata as a passageway to pass between worlds for its own purposes (the thing is Johnny Walker or his spirit). The thing took over Mr. Nakata's body during the Yamanashi incident; came out when Miss Saeki opened the entrance a long time ago. Unable to kill the thing as it slithers toward the entrance stone, Hoshino realizes he needs to flip the entrance stone to close the entrance. With the entrance closed, killing the thing is very easy. He chops it to pieces and burns them.
He vacates the apartment leaving Mr. Nakata’s body aiming to make an anonymous call to the police for them to came and take care of the body and contact Mr. Nakata’s relatives.
Mr. Nakata restores some things & finishes others
When he re-enters our world, Kafka goes back to Tokyo to finish high school; to begin anew his journey toward adulthood. His place as the killer of Johnny Walker was taken up by Mr. Nakata whose body was taken over. Mr. Nakata dies, perhaps going to a world that does not bewilder him. He is reincarnated in Hoshino, who now can talk to cats and close the entrance. Miss Saeki goes to a place beyond the flow of time where she wanted to go a long time ago to maintain, in a static state, the happiness she knew as a 15 year old. In our world, Kafka remains to remember her. At the Komura Library, she is replaced by Oshima as Head Librarian. Johnny Walker finds himself in purgatory, where he can’t harm other people or cats. And we have to believe that Colonel Sanders awaits his next mission in this world, an invisible floating spirit. Finally, Hoshino goes back to Nagoya a different man–all thanks to the influence of Mr. Nakata who continues living through Hoshino.
(The End)
Very thorough summary!