The doctor lands his TARDIS in London, 2010. Nearby are some ordinary looking boys playing football in the street. He engages them in conversation during which one of them, 'Spike', offers the Doctor a crisp from a brightly coloured packet. They have a brief conversation during which Spike and his friends manage to explain Einstein's Theory of Relativity. Perplexed, the Doctor speaks to Spike's mother who tells him that their manifest increase in intelligence is due to the Brainy Crisps they are eating. When he casually mentions his TARDIS is having problems with a virus that seems to be operating throughout the internet she remarks that she left school with only two GCSEs before adding that once he has control of the Space-Time Gap he can access the Vortex and travel through time. Perplexed he heads to the nearest supermarket.
Brainy Crisps are on sale among all the other snack foods. The Doctor buys every packet in the shop. A woman in the checkout queue begins talking to him about how many reward points he can earn from the supermarket before explaining, in detail and with statistics, how the global economy works.
The Doctor takes two trolley loads of crisps back to the TARDIS and analyses them. His tests show that they contain Krillitane oil and the packet reveals the whereabouts of Brainy Crisps' head office.
Soon, he is at the offices and by dexterous use of his sonic screwdriver he installs himself as Doctor John Smith, Strategy and Workflow Manager. He is given his own office and a secretary and finds that within minutes he has been accepted into the company and already has dozens of internal emails. He leaves his secretary to deal with these and goes to a Management Team Meeting. This is run by Stella Stark who runs through the monthly budget figures. The Doctor finds himself stifling his boredom until he notices an inordinate amount of money is being spent on the Computer Department. When the firm's chairman, Sir Manning Cross, congratulates the team on the last month's sales figures the Doctor asks him about the computer figures but he is merely told to consult Henry, the manager of the computer systems.
After the meeting Stella Stark and Sir Manning speak briefly about the Doctor. Neither of them hired him and they wonder who he is and what he wants, though Stella thinks he looks harmless enough. They decide to let Henry deal with him.
Henry, the Director of Computing, confesses to the Doctor that he has been promoted out of his comfort zone. While very good at the system side of things he is uncomfortable with his management role. He brings his young assistant Jeff to the meeting and together they show the Doctor that most of the computer power is used on the Brainy Crisps website. This is where people who have eaten the crisps can test their intelligence to see how much it has improved. The Doctor decides to take the test and finds that after a few questions it becomes a research site on the nature of evolution. The Doctor realises that this is a program that was not devised by humans.
In an effort to get into the management systems which even Henry can't access they realise that they need to use Sir Manning's personal computer. So, after the offices have closed for the night, Henry and the Doctor go up to Sir Manning's office and the Doctor begins breaking the digital deadlock seal to find out what is really going on. They leave Jeff in the IT office, monitoring the system so that he can warn the Doctor if anyone detects his activities. Henry goes to his own office to run some of the accounts programs while the rest of the system is down.
Jeff is suddenly aware that someone has entered the otherwise dark office where he is at work. The visitor is familiar to him until it changes shape to a creature with leathery wings and attacks him, slashing him to death with sharp claws.
When Henry returns to the Doctor's side he is told that the only information the Time Lord has gleaned is of a company meeting the following morning. It is a secret meeting in a posh hotel and does not appear in Sir Manning's company diary. Henry asks him what all this secrecy is about and why they are sneaking about in the dark after hours. The Doctor tells him that he thinks aliens are using Brainy Crisps to further their own ends. The Doctor has begun to search through the office and has just opened a side door when Henry asks him what the aliens look like. The Doctor points to the Krillitane hanging from the ceiling of a secret room. The creature opens its eyes so they turn and run. The creature almost catches them until the Doctor holds it off with a blast from a fire extinguisher. They run down to warn Jeff but only find his corpse. Henry begins to cry at the sight of his dead colleague and the Doctor wonders if Krillitanes can produce tears to order. Henry asks how the monsters can be stopped and the Doctor says he has eighty three bags of crisps in the TARDIS.
Arriving at the hotel at six o'clock the next morning, the Doctor and Henry find that the meeting is to take place in the ballroom. This has been prepared for a silver wedding celebration that evening. A long table stands in the centre of the room but above it hangs a net full of balloons. Left to themselves they make a few arrangements of their own and are just finishing when Gabby arrives. She is one of the employees at Brainy Crisps and 'alright' according to Henry. Nonetheless they both hide from her. When the people arrive for the meeting soon after it is Gabby's job to hand out folders and tea or coffee. She leaves before the meeting begins.
Stella Stark and Sir Manning Cross sit at one end of the table with various managers. The rest of the chairs are taken by major shareholders in the company. It soon transpires that these latter are annoyed that the company's profits are not being passed on to them. Sir Manning quietly explains that the company is his to run how he likes. He does not want it to make a profit; it is now using the internet to infect every computer that uses their website. The goal is to use all that power to solve the riddle of life itself. The Doctor turns to Henry, explaining that the Krillitanes are trying to create a new genetic form of themselves to build a new empire.
The air around the managers shimmers and eight Krillitanes are revealed where their human guises stood. The Doctor takes this as his cue and steps forward to ask a question: are the Krillitanes planning to use Earth as the first step in their plan to take over the universe? He then gives them their customary final warning but when this is laughed at he tells the human shareholders to run. Henry releases the balloons and the contents of eighty three bags of Brainy Crisps. As these touch the Krillitanes their skin begins to burn with the contact of the Krillitane oil. The Doctor opens the door and lets out the shareholders before following with Henry and locking the door.
Gabby asks them what is happening but they hustle her out of the building. Behind them the Krillitanes start to break the door down. Outside the hotel Gabby demands an explanation but the Doctor points out that she has lost an earring. He holds up the missing one and says he found it in Jeff's hand the previous night. Gabby transforms into a Krillitane. Henry pushes her off balance and the two men run down the street and leap into a taxi, giving the address of the Brainy Crisps factory.
The guard at the gate tells them that the other managers have already arrived and the Doctor reminds Henry that the Krillitanes can fly. Inside the factory they find six murdered security guards. Beyond them is a huge hangar-like building with enormous vats. This is where the new breed is being made. The Doctor leads Henry to an office, telling him that the new bodies may already be complete but the brains will need programming. He explains a plan and the two of them access the factory's online programming system. The Doctor leaves Henry to his work and creeps back through the factory. He is just pointing his sonic screwdriver at a valve that will release Krillitane oil when his hand is grabbed and he turns to face the Krillitanes.
At first they mock him for failing in his plan to stop them. Then they grow suspicious and wonder where Henry is. As they search for him it dawns on them that the Doctor allowed himself to be caught to buy time for Henry. Soon the two men are standing beside a large tank from which a loud hammering can be heard. Claws rip open the tank from within and three new Krillitanes emerge. They are three metres tall, red in colour and have faces which are almost human. Sir Manning tells them to kill the Doctor but when the nearest creature reaches out its claws it is to shake the Doctor's hand.
The Doctor tells Sir Manning that the wrong data has been put into the new breed's minds. They have learned to be polite and show good manners. When the order to kill is repeated the three 'angel' Krillitane refuse, saying that they would rather play instead. The original Krillitanes launch themselves at the Doctor and the angels step into their path. A fight ensues during which one of the new creatures claws a tank which sprays out Krillitane oil. The creatures it touches burn immediately and the rest of the oil ignites. The Doctor and Henry make it to the door just in time as the whole factory is filled with fire.
By the time Henry and the Doctor have deleted the alien code from the internet it is time for the Doctor to leave. He makes his way back to the TARDIS and bumps into Spike again. The boy is eating crisps, but not the Brainy kind, and when the Doctor greets him Spike blows a raspberry and runs away. The Doctor grins and enters the TARDIS.