In late December 1999, the TARDIS materializes in the offices of Condef, a British defense contractor, and the Doctor interrupts a break-in. One of Condef's employees, George Gardner, discovers that the intruders were not stealing anything, but were instead installing chips from the company Silver Bullet Systems. The Doctor realizes that the gas used to anaesthetise the security guards surpasses Earth's current level of technology, and advises George to go to Harry Sullivan at MI5 if he learns anything further. George soon contacts Harry with devastating news; he has tested an SB chip for Y2K compliance, and it has failed. Earlier in the century, computer programmers decided to drop the number of the century from date calculations in order to save memory space; thus, when the date changes from '99 to '00, computers all over the world will assume that the year has decreased by 99 instead of increasing by 1, and chaos will ensue. Silver Bullet has made its name by promising solutions to the Millennium Bug, and thousands of companies have bought SB chips and now assume themselves to be Y2K-compliant... but on 1 January, 2000, the chips will fail spectacularly. And now it appears that someone is deliberately installing these chips even in companies which did not originally purchase them.

George tries to run further tests on the chip at home, but the chip detects illicit tampering and sends a pulsed signal through his electrical wires. The staff of Silver Bullet use the embedded chips in his ordinary household appliances to strike out at him, sending a cripplingly high-pitched whine through his phone line and causing his toaster to overheat and set his house on fire. George barely escapes with his life, and retreats to a bunker in the country which he had already furnished to sit out the millennial chaos. Harry, meanwhile, is contacted by Silver Bullet's PR official, Andi Cave, who claims to have similar suspicions about SB's Y2K-readiness; she asks him to investigate rumours of suspicious meetings between Condef employees, a Russian colonel, and General Randall, Britain's NATO liaison.

The Doctor investigates at Condef and learns that Randall has been meeting with Colonel Krimkov, who is in charge of Russia's nuclear deterrence and early warning systems. His attempts to speak with Randall get him nowhere, but Andi Cave then contacts him and takes him to meet James Bryant, a spin doctor for the current government. Bryant suggests that Randall is up to something sinister, and advises the Doctor to back off so Bryant can deal with Randall without attracting attention. Meanwhile, Harry investigates an attempt to break into Ashley Chapel Logistics, and discovers that the only possible target for the raid was a collection of software and hardware which ACL had purchased from the defunct company I2. The Doctor and Harry realize that, once again, the Voracians -- hybrids of alien reptiles and malevolent office equipment -- are attempting to conquer the Earth.

The Voracians have already converted a number of government and military officials to the cause, and are attempting to track down and reassemble the scattered code fragments of the AI software Voractyll. They have allowed one of their programmers, Dave Hodges, to remain fully human in order to use his intuition and emotional judgement; however, when the curious Hodges takes a peek at the software code he's assembling, they decide he's gone too far and convert him into a cyborg to ensure his obedience. This decreases his productivity, however, and the Voracians are forced to concentrate their efforts on recovering the pen which Sarah Jane Smith had acquired during her encounter with the Voracians. Unaware that it contained a tracking device, she had kept it as a souvenir and later given to Harry, and the chip within may contain enough Voractyll code to complete the programme.

The Doctor breaks into Silver Bullet and overhears its CEO, Byron Cutter, discussing the recovery of the pen. When he mentions this to Harry, Harry realizes what pen they mean too late; SB employees have already broken into his home and taken the pen, and in the process have nearly killed Sylvia Webb, the young woman who cleans house for him. Harry arranges for Sylvia to receive hospital care, blaming himself for her condition, and he and the Doctor then concentrate their efforts on Randall. Harry has learned that Randall is in charge of the military forces which will be called into play to see the public through the worst of the Y2K disaster, and the Doctor has realized that he's been followed by soldiers from Randall's squad ever since trying to speak with him. They conclude that Randall is involved in Silver Bullet's plan to exacerbate the Y2K disaster in order to create an excuse to stage a military coup and take over Britain.

The Doctor visits George Gardner, who has run further tests on an SB chip -- without connecting it to an external power line -- and has found a way to shut down individual SB chips. Meanwhile, Harry is contacted by Mike Foley, a CIA agent who advises him to speak with the Deputy Prime Minister, Philip Cotton; the current PM, Terry Brooks, got his seat by making promises about social programmes and education which he simply doesn't have the budget to back up, and has recently been holding secret meetings to which the openly critical Cotton has not been invited. Harry meets with Andi Cave to tell her his suspicions about Randall, but discovers that she is a Voracian and is forced to flee. Meanwhile, the Voracians find that the security software on the chip inside the pen has become corrupt, and decide not to install it until the last moment; that way, if it interprets their attempt to access it as an attack and shuts itself down, they will at least be able to snapshot the data and reconstruct it.

Defense Secretary Jennifer Hamilton has second thoughts and tries to back out of the PM's potentially devastating plan, but she is shot and killed and Harry is framed for her murder. When Harry and the Doctor visit Sylvia in the hospital, she calls in the police and they are forced to flee. Foley rescues them and takes them to meet Randall, and upon learning that they have escaped, Cutter and Bryant arrange for Sylvia to be taken hostage to ensure their good behaviour. The Doctor and Harry, meanwhile, learn that Randall has no intention of staging a coup, although someone is trying to make it appear as though he does. Randall explains that he met with Krimkov to discuss the Russian response to Y2K; if the obsolete Russian defense system suffers catastrophic shutdown and the commanders of its nuclear bases are rendered blind, the result may be an accidental nuclear exchange. The Western military, after some consideration, has agreed to supply Russia with up-to-date defensive equipment to avoid any such difficulties, but thanks to Silver Bullet, the equipment which the West has supplied to Russia has been deliberately engineered to fail...

Cotton and Foley reveal that Randall's organisation has a traitor in its midst, which is why Cotton went to the CIA for help when he came to suspect Brooks was plotting against his own government. Thanks to the proliferation of defunct SB chips, Randall will be forced to fill the streets with his soldiers, and once the crisis has passed, he will be accused of attempting to stage a coup. Brooks intends to take advantage of the ensuing public outcry to cut funds to the military and put them into the social programmes he had promised. What he doesn't realize is that the SB chips will then be used to create a virtual network through which Voractyll will be released into the world once again, enabling the Voracians to seize control.

The Doctor determines that the traitor is Lieutenant-Colonel Attwood, but Randall decides not to reveal his knowledge to Attwood just yet. Harry and Foley contact Krimkov to inform him of the SB situation, and Krimkov informs them that rebels in Krejikstan have stolen a nuclear warhead and are now attempting to seize control of the nuclear base at Nevchenka in order to launch it at Moscow. Foley agrees to send American troops to help defeat the rebels, in exchange for help exposing Brooks' machinations. Foley then arranges for an assault team to break into Silver Bullet Systems to rescue Sylvia, who has been sent to the operating theatre to be transformed into a Voracian after being caught trying to escape; Foley's troops break her out almost literally from under the operating knives.

It is now New Year's Eve, and as midnight approaches, Sylvia recovers from her ordeal, Randall's troops search their equipment for embedded SB chips and the Doctor converts George Gardner's programme into one he can download from his sonic screwdriver. At midnight GMT, 1 January 2000, London is crippled by power failures, bank machines refuse to distribute cash, and the traffic system goes haywire. Air traffic controllers lose radar, runway lights, transponder codes and satellite navigation. The troops heading for Nevchenka are forced down by autopilot and GPS failure, stranding them over an hour's flight away while Lieutenant Ivigan and his men try to hold off the rebels from a facility which has just lost power to the electric fences. Randall's men are suddenly required everywhere in London to help emergency forces and supply food and medical equipment, and he can barely afford to spare the men the Doctor needs to stop the Voracians.

The Doctor finally realizes that the I2 pen was given to Sarah as a tracker, which means it must be transmitting a signal which he can use to locate it. He discovers that it has been moved out of the Silver Bullet offices, but before he can narrow down its location Sylvia unexpectedly attacks him and smashes the tracing equipment. Harry is forced to shoot her, realizing that she was rescued too late and had already been transformed into a Voracian. Emotionally drained, Harry continues on to Downing Street, where the Doctor joins him after completing his work on George's programme. Not only can he shut down any such chips, he can emulate the Millennium Bug in systems which don't suffer from it.

Randall's men fight their way past Attwood's Voracian troops and take over 10 Downing Street, and both Attwood and Cave are killed in the fighting. Foley, Randall and the Doctor then inform Brooks about the deal with Krimkov and allow him to contact the Russian Premier, who tells the horrified Brooks that a missile has been launched from Nevchenka due to the British having supplied faulty detection equipment. As the Premier prepares to launch a retaliatory strike Brooks breaks down and admits the truth, and realizes too late that he has been tricked and that his confession has been broadcast to his own Parliament. His career is now magnificently over, and as he has nothing left to lose, the Doctor insists that he reveal where Cutter has gone. Bryant attacks Brooks, trying to shut him up, and when Bryant is shot and revealed to be an alien cyborg, Brooks admits that Cutter has set up in Chequers, the PM's private country residence.

Realizing that a show of force will provoke the Voracians into activating Voractyll ahead of schedule, the Doctor and Harry go to Chequers alone, and Harry creates a distraction while the Doctor breaks in. The Doctor finds Dave Hodges about to install the missing code sequences and activate the programme, and tries to reawaken his buried humanity. He is captured, as is Harry, and when Hodges refuses to activate Voractyll, one of the Voracians kills him and activates it. Thanks to the Doctor's continued attempts to distract them, however, the Voracians have neglected to check the programme for faults -- and they realize too late that the Doctor has programmed it to emulate the Millennium Bug. The Voracians shut down or explode as the bug hits them, and Voractyll is destroyed, ending the invasion.