It picks up where The Girl Who Played with Fire left off, two rooms away from her also-injured father, Alexander Zalachenko, whom Salander injured with an axe.

These events prompt immediate action from "the Section", a secret counterintelligence division of Säpo which shielded the abusive Zalachenko and forcibly institutionalized Salander after she attempted to kill him as a child.

Evert Gullberg, founder and former chief of the Section, plots to deflect attention by silencing Salander, Zalachenko, and Mikael Blomkvist, the publisher of Millennium magazine.

Meanwhile, Dr. Peter Teleborian, the corrupt psychiatrist who abused Salander during her institutionalization, provides prosecutor Richard Ekström with a false psychiatric examination so that she can be recommitted.

Other operatives break into Blomkvist's apartment and mug Giannini, making off with copies of the classified Säpo file that contains Zalachenko's identity and planting bugs in the homes and phones of Millennium staff.

Blomkvist arranges to have Salander's handheld computer returned to her, and has a cellular phone placed in a duct near her room to give her an online hotspot through which to maintain contact with the outside world.

Meanwhile, Blomkvist, Armansky, and their allies continue their joint counter-surveillance of the "Zalachenko club", feeding them misinformation about Millennium's (supposed) passivity regarding Salander's trial, identifying nine central players in the Section.

The Section catch on to the ruse and arrange to plant cocaine in Blomkvist's apartment and hire two members of the Yugoslav mafia to murder him; their intention is to frame him as a drug dealer and thus destroy his credibility.

Giannini systematically destroys Teleborian's testimony, proving that he and the Section conspired to commit Salander to protect Zalachenko and that his recent "psychiatric assessment" of her was fabricated.

"[11] On Bookmarks, the book received a 3.5 out of 5 with the critical summary saying, "After all, The Girl Who Kicked the Hornet's Nest has its share of faults--including clichéd, workmanlike prose; tangled plots; and tedious repetition.

[16] The Los Angeles Times disagrees, describing the plots as "improbable", but notes the popularity of the series, referring to it as "an authentic phenomenon".

[18] The Los Angeles Times critic agrees, pointing at the implausibility of Larsson's plot, the weak writing and characterisations.