Blue Box tells the story of how Sarah Swan ended up in Bainbridge Hospital, where the American government keeps mental patients who know too much to be let out in public. Her story has been written by investigative journalist Charles “Chick” Peters, an expatriate Australian living in America. Chick was not privy to all of the information, and in addition, some of the facts have been changed, including Sarah’s real name and her employer.

The story begins in Washington, D.C., in Christmas of 1981. An American college student named Peri Smith (not her real name) has been travelling with an Englishman named the Doctor, who’d promised to take her home to her family and had even dressed in a tailored black suit for the occasion, rather than his usual multicoloured patchwork coat. However, they’ve arrived at the wrong time and in the wrong part of the country, and then the Doctor disappears while Peri is eating at a children’s restaurant. At first Peri fears that he’s been kidnapped and that she too may be in danger, but after a day he telephones her at her hotel and orders her to contact Bob Salmon, a young sysop for the local university, who once helped the Doctor to extract a back door installed in government software by a corrupt programmer. However, even Bob is shaken when the Doctor informs them that he wants them to steal something from Sarah Swan.

Swan is a hacker and phreak who now works for TLA, an important defence contractor -- and she’s legendary for her ability to hack into any computer system and destroy the lives of anyone who crosses her. Nevertheless, Bob and Peri nevertheless make some fake phone calls, convincing TLA’s supplier Keyworth Computers that TLA has ordered a new Lisp machine, and telling TLA’s receptionist that this is a rush delivery job with no invoice. However, the receptionist is more efficient than they’d expected, and she double-checks the order with Swan herself. Swan watches Bob set up the computer, and he and Peri are forced to leave without any information on the device the Doctor wants stolen. Swan takes a photograph of their van, intending to track them down and find out who they really are and what they want.

Chick learns of the bizarre “crime” on a date Trina, Keyworth’s receptionist, and arranges to speak with Swan, who agrees to let him have the story as long as he disguises her identity. Chick thus calls his contact Ian Mond, a hacker who once fell foul of Swan and has been living in a hell of cancelled credit cards, false alarms to 911 and fake pizza deliveries ever since, constantly forced to move whenever she tracks down his new address and phone number. Swan has identified the van as university property, and Mond identifies Bob Salmon as the only employee with the know-how to pull a stunt like this. He thus drives Chick to Bob’s home and wiretaps his phone so they can learn more. The Doctor eventually contacts Peri and Bob, but claims that the people he’s working for won’t let him get anyone else involved. He realises that the phone is being tapped, and Peri and Bob try to flee, but Chick follows them to a local mall, makes contact and assures them that his interest is purely neutral; as long as they let him in on the story, he won’t tell Swan where to find them.

When the Doctor next contacts them, he agrees to speak with Chick, presumably in order to keep an eye on him. Chick meets the Doctor in a downtown hotel, where he watches as the Doctor uses a modified Apple II+ to hack into the TLA mainframe and snoop around. It’s Christmas Eve, but Swan is still at work, and she catches him and kicks him out -- but the Doctor promptly logs himself back in with access to the root account, logs off Swan herself, and downloads her e-mail. As he and Swan do battle electronically, Bob and Peri break into TLA again and wait for word from the Doctor, who finds the clue he needs in Swan’s e-mail -- the device he needs is in the cellar of TLA. Swan gives up, physically disconnects her computer from the ARPAnet, and then checks on the device to make sure it’s safe, unwittingly leading Bob and Peri right to it. Bob and Peri smuggle the device out of TLA and back to Bob’s home, where the Doctor and Chick are waiting. Bob is surprised to find that the Doctor has changed since their last meeting. Peri is still upset at being left out, but the Doctor explains that the people he’s working for didn’t leave him a choice. Also, there’s a second device still out there somewhere.

The Doctor decides not to return the device until he’s had a chance to look it over himself, but he does agree to take Chick to a meeting with his contact, Mr Ghislain. Ghislain, a bland-faced man accompanied everywhere by a parrot, explains that the Doctor is helping to locate the missing components of an alien super-computer lost on Earth. The people of Eridani don’t have faster-than-light capability, and had dismissed the Earth as an unimportant, primitive world; a robot ship aiming for one of their colonies thus became confused when it began picking up radio transmissions from Earth, and landed there instead. The Eridani have recovered three of the five components already, and the Doctor is helping them to locate the remaining two in order to keep dangerous alien technology out of the hands of the human race. Chick doesn’t believe a word of this sci-fi nonsense, and concludes that these are code terms being used to cover the fact that parts of a prototype Russian supercomputer have somehow become lost in America.

Swan contacts Mond and agrees to stop harassing him if he helps her to locate the people who’ve been interfering in her business. He agrees to do so, but leaves an extremely obvious wiretap at Bob’s house, thus warning him that he’s being watched. The Doctor and his friends retreat to a hotel in Baltimore, but as soon as Bob’s house is empty, Swan breaks in to investigate further. She’s stunned when she sees the abandoned hazmat container she was using to store the Eridani component, proof that her most precious belonging has been stolen from her, and vows to crush her opponents. Noting that Bob owns several books on the occult, she draws up an occult symbol and sticks it to his fridge in order to give him a scare if he returns.

The Doctor decides not to involve the authorities, but Peri has had enough of being frightened and on the run; when this is over, she’s going to leave the Doctor. She and Chick switch cars to throw off pursuit, while the Doctor and Bob try following Swan’s e-mail trail, assuming that she took will have been looking for the final Eridani component. Swan locates their electronic trail and contacts them, threatening to destroy their lives if they don’t back down and tell her about the bizarre device. The Doctor in turn warns her that the devices are too dangerous for her to tamper with, and threatens to inform the authorities of her connection to the death of Charles Cobb. Swan ignores the threat and signs off, and the Doctor decides to tap her phone in order to find out what else she knows. Chick is coming to realise that the Doctor, whether he actually believes in aliens or not, genuinely seems to believe that the planet is in danger and will do whatever it takes to get the missing component.

Bob sets up a tap on Swan’s phone, but then returns home to make sure everything is all right and gets the shock of his life when he sees the sigil stuck to his fridge. Panic-stricken, he rushes back to the hotel, unaware that Swan had staked out his home and is following him. Swan orders flowers for him, watches to see which room they’re delivered to, and then taps the room phone. Eventually, unable to learn anything more from the one remaining component, the Doctor contacts Ghislain and arranges to turn it over -- and Swan makes a note of the address and calls in the police. She bumps into Chick, Peri and Bob on the way out, and they flee, knowing that the Doctor is walking into a trap but with no way to warn him.

In fact, Swan already knows where the final component is. She and her friend Luis Perez bought the two components as a set at an underground auction, and have been trying to puzzle them out ever since. Swan contacts Luis to warn him that someone might be planning to steal his device, but Luis tells her that something amazing has happened -- his device has hatched into a living being like a lump of muscle in the shape of a Y, with tiny cilia-like tentacles for fur. It is disassembling and reassembling pieces of Lego and electronic components as they watch, and they can’t seem to stop watching.

The Doctor is nearly caught by the police, but uses the Eridani component to “persuade” them to let him go. He delivers the device to the Eridani and is reunited with his friends, but sees that Peri is becoming stressed out and admits to Chick that she deserves better than the life she leads with him. Chick still doesn’t believe that the devices are alien in origin, but she politely listens to the Doctor’s admittedly well-thought-out backstory. Bob asks the Doctor about the occult symbol, and the Doctor assures him that it’s probably just a bluff; Swan is unlikely to know any of the psionic rituals known as magic on Earth. Bob is not reassured.

Convinced that Swan has some idea of where to find the last component, the Doctor taps into a phone line in order to keep an eye on her movements. A policeman stops by to investigate the parked cars, takes one look at Chick, orders him and Peri out of the car and then tries to remove Chick’s shirt. Peri and Chick overpower him and steal his police radio in order to make sure they’re not being followed, but for some reason the policeman doesn’t report the incident, almost as though he’s embarrassed by what happened.

The Doctor has learned that Swan intends to visit Ocean City and check out Charles Cobb’s house for more information. Cobb arranged a meeting between the Eridani and an obsessive collector who was hoarding the third component; nobody’s sure who betrayed who, but though the Eridani recovered their component, at the end of it all Cobb, the collector and one of the Eridani were dead. The Doctor hopes Swan will see reason if they speak face to face, but Swan finds her phone has been tapped and phones Luis, claiming to be meeting a contact at the Delaware State Fair. The Doctor, Peri and Chick try to follow her, and by the time they realise they’re on a wild goose chase, Swan has already been to Cobb’s house and downloaded his last week of e-mail. Peri uses a makeshift flamethrower built by the Doctor to torch the house, ensuring that nobody else will be able to use Cobb’s information -- but in fact, Swan had never met Cobb, and only knew of him because the Doctor mentioned him to her earlier. Now, she knows that the thing in Luis’ bathtub is the only remaining component of something so powerful people are willing to kill for it. She thus calls Luis again, and while he’s out of the house, she breaks in and steals the thing in his bathtub.

The Doctor agrees to “meet” Swan in a Multiple User Dungeon, which is normally used for virtual role-playing but now is neutral territory where they can discuss the creature. Swan doesn’t believe it is alien, but she knows it’s more advanced technology than anything else on Earth, and she wants it. All she wants from the Doctor are operating instructions, and she refuses to listen to his warnings, even when Luis storms into the dungeon, hysterically threatening to kill Swan if she doesn’t return the creature. She signs off, and Luis, apparently suffering from a kind of withdrawal, admits to the Doctor that he purchased the “egg” at an auction in Ritchie. The Doctor and his friends visit Ritchie to find numerous people walking about in a daze, as though trying to remember something important. To the Eridani, even the human brain is only a piece of hardware which can be physically restructured to run different software -- and just as the people of Ritchie have been altered by being near the devices, Swan and Luis have been reprogrammed to care for the creature, even more than they care for their own lives.

Bob hacks into Swan’s e-mail and credit card accounts, and determines that she’s wired her home with security cameras and motion detectors and is e-mailing uuencoded pictures to her account at work. Some of the pictures indicate that there’s something living in Swan’s bathtub. Still unsure of the true nature of the device, the Doctor contacts Ghislain, who explains that it has the ability to hack into and reprogramme any computer hardware, including the human brain. In effect, it’s like an idiot savant with a talent for hacking computers -- and it’s born with the ability to reproduce itself. If it gets out of Swan’s limited control, it could wreak havoc within the Earth’s primitive computer systems.

Swan watches the creature as it studies her computer, writes a programme from scratch, tests and debugs it, and then goes back to playing with Lego. Unable to concentrate on her own work while the Savant is near, she mails a copy of the programme to her work account, tears herself away from the Savant and goes to work to study the programme there. Bob breaks in, gets a copy of the programme and e-mails it to the Doctor, but Swan catches him and has him arrested for illegal entry. Bob’s father bails him out, and although he’s upset with the Doctor for landing his son with a criminal record, Bob manages to convince him that they’re working to prevent a hacker from seizing control of potentially every computer connected to the ARPAnet. As the net continues to expand, that cold mean thousands of computers over the next thirty to forty years. Mr. Salmon reluctantly agrees to let Bob continue with what he’s doing.

Still unnerved by the occult symbol he found on his fridge, Bob designs his own and gives it to the Doctor for protection. The programme he copied from Swan’s computer then begins running on the Doctor’s Apple, but the Doctor switches it off before it can make more copies of itself. He then tracks down Swan, who’s still convinced the Savant is a secret government project and is searching the net for some trace of its manual. She offers to drop charges against Bob if the Doctor tells her how it works, but signs off when the Doctor only repeats his warnings. Desperate, she contacts Chick and demands to know what he’s learned about the Doctor, and when Chick claims neutrality, Swan furiously calls him a faggot. Chick thus decides which side he’s on, waits until Swan’s at work and breaks into her house to steal the Savant, but he can’t stop looking at it, and it keeps him entranced until Swan shows up to protect it. When he tries to take it from her, he relives the one time he took angel dust, a memory so powerful reliving it nearly kills him. Chick retreats, and Swan strikes back by calling his editor and revealing that Chick was fired from his job on the west coast, possibly for punching an editor who called him gay.

Luis is now barely functional, both hating the Savant for what it’s done to him yet desperately needing to have it back. The Doctor realises that Luis may be beyond saving, but he’s the only one who can get close to the Savant now without being attacked like Chick was. The Eridani send the Doctor an interrupt programme which will shut down the Savant if necessary, but the Doctor intends to use this only as a last resort, as he’s unsure what effect it will have on Luis or the people of Ritchie.

Due to Chick’s failed break-in attempt, Swan now believes that it’s safe to leave the Savant alone, and Luis thus successfully steals it after Bob cuts the security camera feed. On their way back to the hotel, however, the Doctor and his friends see that they’re being followed by Ian Mond. Chick goes back to Ian’s car to find out what he wants, but Swan is in the back seat with a shotgun. Ian flees as Swan tries to retrieve the Savant, and the Doctor has no choice but to operate the Interrupt. The Savant freezes up, Luis goes limp, and Swan nearly shoots them all in a fit of rage; however, instead she drags Luis back to Mond’s car and drives him back to her home. There, she sits and watches as he plays with Lego.

Swan calls the university and threatens to involve them unless they take action against Bob; however, the Doctor has been expecting her to seek revenge and has forwarded the call to Bob’s father, who pretends to be Bob’s supervisor and thus buys his son a few days’ leeway. Chick isn’t so lucky; Swan has finally learned the truth about him, and she presents Chick’s editor with proof. Chick’s editor calls his home to demand an explanation, and the Doctor, Peri and Bob all hear the message he leaves on the machine. Though Chick is genetically male, his body does not respond to male hormones, and, at least on the outside, Chick’s a woman. He insists that he’s male, but society doesn’t agree, and now it appears his life has been ruined again.

The Doctor doesn’t particularly care about Chick’s secrets; all he is interested in is finding out why Swan kidnapped Luis and what the Savant’s programme does. The programme tries to copy itself out of Swan’s system, but the Doctor, Bob and Peri break into her house and physically disconnect her computer before it can spread itself through the ARPAnet. While they’re gone, Swan contacts Chick and demands to meet him at a restaurant. She’s sitting in a booth with Luis when Chick arrives, and Chick watches in horror as Swan orders the waitress to bring them $100 bills straight from the till -- and the waitress obeys unquestioningly, her eyes glazed like the people in Ritchie. With Luis at her side, Swan can hack any system, even the human brain, and she’ll soon have total control over the only world she cares about -- the world inside the computer.

Chick, shaken and terrified, tells Swan all about the Doctor’s bizarre story of aliens, and Swan allows him to leave. Chick then calls the Doctor, who realises that the Savant’s computer programme is a copy of the Savant itself, a self-replicating programme capable of adapting itself to any system. When the Doctor tried to shut down the Savant, it simply copied itself into Luis’ brain, overwriting the “instructions” which were already there. If he tries to use the Interrupt again, the Savant will simply copy itself into the nearest person. It may not even need to be in danger to replicate, which is why everyone it encounters seems dazed and disoriented afterwards; there’s a dormant copy of the Savant inside their brains, taking up most of their mental functions and awaiting only a trigger to activate fully. If Swan keeps using Luis for her own ends, the Savant’s “eggs” will spread exponentially until the Earth is a world of zombie computers waiting for the Eridani to arrive and harvest them.

The Doctor calls Swan on the pay phone next to her car and gives her one last chance to see reason, but he’s unable to prove his claims and Swan hangs up on him. She and Luis then walk into a bank and walk out with enough money to get out of Washington and start up elsewhere. However, traffic on the Cabin John Bridge is snarled up, and according to Swan’s police scanner it’s due to a roadblock set up to catch her. Swan thus takes a detour only to spot the Doctor waiting for her, having used his stolen police radio to broadcast a fake message and drive Swan into his path. Furious, Swan orders Luis to fry the Doctor’s brain once he’s close enough. The Doctor flees out to Great Falls Park, which is all but deserted at this time of year, but he has underestimated the Savant’s power and nearly leaves it too late to use the Interrupt signal. Fortunately, as the Savant launches its attack, the occult symbol which Bob drew for the Doctor falls out of his pocket before his eyes. The symbol is completely meaningless, giving the Doctor nothing to focus on consciously, and in this moment of distraction the Doctor operates the Interrupt signal. The Savant tries to copy itself into Swan, but the Interrupt signal shuts down that copy as well; the Doctor only survives because the Savant momentarily has nothing to latch onto in his conscious mind.