The novel is divided into two parts.
Part 1: "Underground"
It consists of an introduction, three main sections and a conclusion. (i) The short introduction propounds a number of riddles whose meanings will be further developed. (1) Chapters two, three and four deal with suffering and the enjoyment of suffering; (2) chapters five and six with intellectual and moral vacillation and with conscious "inertia"-inaction; (3) chapters seven through nine with theories of reason and logic; (c) the last two chapters are a summary and a transition into Part 2.
War is described as people's rebellion against the assumption that everything needs to happen for a purpose, because humans do things without purpose, and this is what determines human history.
Secondly, the narrator's desire for happiness is exemplified by his liver pain and toothache. This parallels Raskolnikov's behavior in Dostoyevsky's later novel, Crime and Punishment. He says that, due to the cruelty of society, human beings only moan about pain in order to spread their suffering to others. He builds up his own paranoia to the point he is incapable of looking his co-workers in the eye.
The main issue for the Underground Man is that he has reached a point of ennui and inactivity. Unlike most people, who typically act out of revenge because they believe justice is the end, the Underground Man is conscious of his problems, feels the desire for revenge, but he does not find it virtuous; this incongruity leads to spite and spite towards the act itself with its concomitant circumstances. He feels that others like him exist, yet he continuously concentrates on his spitefulness instead of on actions that would avoid the problems he is so concerned with. He even admits at one point that he’d rather be inactive out of laziness.
The first part also gives a harsh criticism of determinism and intellectual attempts at dictating human action and behavior by logic, which the Underground Man mentions in terms of a simple math problem two times two makes four (see also necessitarianism). He states that despite humanity’s attempt to create the "Crystal Palace," a reference to a famous symbol of utopianism in Nikolai Chernyshevsky’s What Is to Be Done?, one cannot avoid the simple fact that anyone at any time can decide to act in a way which might not be considered to be in his or her interests; and some will do so simply to validate their existence and to protest and confirm that they exist as individuals. For 'interests' as a general term is subjective and in the case of the Underground Man the good here he's ridiculing is enlightened self-interest (egoism, selfishness). It is this latter position being depicted as logical and valid that the novel's protagonist despises. Since his romantic embracing of this ideal, he seems to blame it for his current base unhappiness. This type of rebellion is critical to later works of Dostoyevsky as it is used by adolescents to validate their own existence, uniqueness, and independence (see Dostoyevsky's The Adolescent); rebellion in the face of the dysfunction and disorder of adult experience that one inherits when reaching adulthood under the understanding of tradition and society.
In other works, Dostoyevsky again confronts the concept of free will and constructs a negative argument to validate free will against determinism in the character Kirillov's suicide in his novel The Demons. Notes from Underground marks the starting point of Dostoyevsky's move from psychological and sociological themed novels to novels based on existential and general human experience in crisis.
Part 2: "Apropos of the Wet Snow"
The second part is the actual story and consists of three main segments that lead to a furthering of the Underground Man's consciousness.
The first is his obsession with an officer who physically moves him out of the way, seemingly without noticing his existence. He sees the officer on the street and thinks of ways to take revenge, eventually deciding to bump into him, which he does, finding to his surprise that the officer does not seem to notice that it even happened.
The second segment is a dinner party with some old school friends to wish Zverkov, one of their number, goodbye as he is being transferred out of the city. The underground man hated them when he was younger, but after a random visit to Simonov’s, he decides to meet them at the appointed location. They fail to tell him that the time has been changed to six instead of five, so he arrives early. He gets into an argument with the four after a short time, declaring to all his hatred of society and using them as the symbol of it. At the end, they go off without him to a secret brothel, and, in his rage, the underground man follows them there to confront Zverkov once and for all, regardless if he is beaten or not. He arrives to find Zverkov and company have apparently already retired with prostitutes to other rooms. He then encounters Liza, a young prostitute, with whom he goes to bed.
The story cuts to Liza and the underground man lying silently in the dark together. The underground man confronts Liza with an image of her future, by which she is unmoved at first, but, she eventually realizes the plight of her position and how she will slowly become useless and will descend more and more, until she is no longer wanted by anyone. The thought of dying such a terribly disgraceful death brings her to realize her position, and she then finds herself enthralled by the underground man’s seemingly poignant grasp of society’s ills. He gives her his address and leaves.
After this, he is overcome by the fear of her actually arriving at his dilapidated apartment after appearing such a "hero" to her and, in the middle of an argument with his servant, she arrives. He then curses her and takes back everything he said to her, saying he was, in fact, laughing at her and reiterates the truth of her miserable position. Near the end of his painful rage he wells up in tears after saying that he was only seeking to have power over her and a desire to humiliate her. He begins to criticize himself and states that he is in fact horrified by his own poverty and embarrassed by his situation. Liza realizes how pitiful he is and tenderly embraces him. The underground man cries out "They—they won't let me—I—I can't be good!"
After all this, he still acts terribly towards her, and, before she leaves, he stuffs a five ruble note into her hand, which she throws onto the table. He tries to catch her as she goes out to the street but cannot find her and never hears from her again. He tries to stop the pain in his heart by "fantasizing", "And isn't it better, won't it be better?...Insult — after all, it's a purification; it's the most caustic, painful consciousness! Only tomorrow I would have defiled her soul and wearied her heart. But now the insult will never ever die within her, and however repulsive the filth that awaits her, the insult will elevate her, it will cleanse her..." He recalls this moment as making him unhappy whenever he thinks of it, yet again proving the fact from the first section that his spite for society and his inability to act like it makes him unable to act better than it.
The concluding sentences recall some of the themes explored in the first part, and the work as a whole ends with a note from the author that while there was more to the text, "it seems that we may stop here."