The main theme of Notes from Underground is reason against freedom: the book argues that calculation and self-interest do not exhaust man, and it shows the price of that defense, because whoever rejects the table and the Crystal Palace is left with nothing to put in its place.
The underground man has everything he needs to act, with lucidity, argument, and opportunity, and does not act, because consciousness gives him back, for every cause, another cause. The way out he offers is caprice, the independent will, which proves freedom only when it goes against one's own interest, and this repeated proof turns into the suffering that, he says, man loves as much as well-being.
Six themes revolve around this core. Reason is the target of Part One, with Twice Two and The Crystal Palace. Fate and free will is the dispute with The Stone Wall and The Piano Key. Suffering is, for him, the cause of consciousness. Action and inaction appear in the conscious inertia of Chapter XI. Pride and love dominate Part Two: the wounded vanity that makes the narrator someone who knows only how to tyrannize whoever comes close to him, and who cannot bear to be embraced by Liza.