Apparently teaching Physics at the school, the Time Lord ponders the subject before asking his students a question. The only one willing to reply is a boy named Milo, who gives the correct answer. The Doctor then asks another question and as before, it is only Milo who gives a response. He begins testing the student with increasingly difficult questions; ultimately discovering he understands how to travel faster than the speed of light.
At lunchtime the children and the Doctor shuffle along in the canteen cue, where Rose is now working as a dinner lady. She stares at her friend with an unimpressed look and he smiles back at her before wandering off to find a seat. Later on, as the room is clearing, Rose walks over to clean the Doctor’s table. He teases her as she mops up and moans about her new job. The Time Lord protests, claiming it is Mickey’s fault they are at the school, for it is he who summoned them to investigate strange goings on. He claims he was right to do so and tells her about Milo, stating he has knowledge far in advance of human understanding.
Conversation then turns to the school dinners, and the Doctor comments about the odd tasting chips. He then ponders the behaviour in the school, remarking how strangely obedient the children are. His musings are interrupted when another dinner lady appears. She tells Rose to return to the kitchen and in response to the Doctor’s criticism of the canteen food, claims the menu is specifically designed by the headmaster to improve concentration and performance in the students.
Elsewhere in the canteen another teacher, Mr Wagner, approaches one of the students, a girl named Melissa. He tells her she is to join his special class after lunch, and then turns to her friend Kenny, noting that he is not eating the canteen chips. The young boy claims he is not allowed to eat the food and Wagner leaves with Melissa, under the watchful eyes of the Doctor and Mr Finch.
Back in the kitchens Rose observes as her fellow dinner ladies don protective clothing and begin bringing in barrels of oil on a trolley, taking special care not to spill any. As they do this Rose receives a call from Mickey on her mobile phone. Sat in a cyber café he browses the Internet, recounting the UFO activity spotted around the school in recent months. As he searches he discovers a page blocked by a Torchwood Access Barrier, but continues nonetheless. Rose then reveals that three months ago all of the kitchen staff were replaced and new workers introduced, all of whom appear to be acting strangely.
During the conversation the dinner ladies knock over a barrel of oil. The content spills onto one of the party and visibly scalds her. She screams and is hurried into a little office in the corner of the kitchen. Rose hangs up on Mickey and offers to call for an Ambulance but those looking after the wounded woman tell her not to, claiming they can deal with the problem.
In one of the school computer rooms, Mr Wagner orders his students sitting at the workstations to put on their headphones. He then clicks a button on his own computer and the children’s screens light up with strange alien text. They immediately begin typing at a frenzied pace, transfixed by the information before them.
Meanwhile, Mr Finch escorts a female visitor around the school, discussing the changes he has made since his arrival, including the free school dinners programme. Although his visitor worries about working the students too hard, the pair agrees good exam results are worth the effort. They then walk off to examine the school further.
In the staff room the Doctor talks to a teacher named Mr Parsons about the cases of extreme intellect developing in students around the school. Parsons notes that the strange activity began when Mr Finch arrived. Within weeks of his employment half of the staff caught the flu and were replaced. The Doctor’s predecessor on the other hand left after winning the lottery, despite never having played it in her life – the winning ticket was posted through her letterbox.
Mr Finch arrives with his guest, whom he claims is writing an article on the school. The Doctor is amazed to find that the woman is Sarah Jane Smith, his former companion. Finch leaves to allow Miss Smith to talk with the staff, and she begins by introducing herself to the Doctor, now working under the alias of John Smith. Sarah remarks that she once had a friend who went by the same name, and the Doctor claims it is a common one. His old friend retorts, claiming that the man she refers to was far from being common.
The two continue to talk, discussing the new curriculum and the fact that several students have become increasingly ill over the past few weeks. The Doctor smiles uncontrollably and remarks that the reporter appears to be pursuing more than a simple profile of the school. She tells him there is no harm in doing some investigating as well, and he agrees, still jubilant at her presence.
As lessons resume, Kenny finds himself alone in an empty corridor. He hears a strange noise coming from the computer lab and goes to investigate. When he enters he sees a bat-like creature crouching underneath a table. It stands up and takes the form of Mr Wagner, who promptly tells the student to leave.
That night Sarah returns to the school and breaks in via a window. Elsewhere, the Doctor, Rose and Mickey also return to look around. Rose makes her way to the canteen to collect an example of the oil she saw earlier whilst Mickey heads towards the maths department and the Doctor goes to investigate Finch’s office.
As Sarah, the Doctor and Rose make their separate ways around the building they each hear a piercing screech coming from somewhere within the school. Rose manages to collect her oil sample from the kitchen whilst Sarah retreats to a corridor at the back of the school, where she is shocked to discover the TARDIS. She backs away through a set of doors and finds herself in the gym where John Smith, alias the Doctor, is waiting for her.
She is initially rendered speechless by the realisation her old friend has returned, but manages to regain her composure and comment on his new appearance. As the two begin to talk they discover they both have come to school for the same reason – to examine the localised UFO activity. Overcome by emotion Sarah remarks how the Doctor never came back to meet her once he dropped her off on Earth, despite his promise to the contrary. Suddenly a scream is heard and the reunited friends run off to investigate.
Running into another corridor they find Rose, who has also heard the shriek. The Doctor introduces his current travelling companion to his old friend. They begin to spark off of each other but the Doctor interrupts their comments and insists they find the source of the scream. They continue running through the school and eventually arrive in the maths department, where they discover it is Mickey who yelled, having found a store of vacuum packed dead rats in a nearby cupboard.
Whilst the Doctor belittles Mickey for screaming like a girl, Sarah and Rose argue as to why the rats are being stored in the school, and end up goading each other about the difference in their. Again the Doctor cuts in to silence them by claiming they must visit Mr Finch’s office, as it appears all of the strange goings on in the school have begun upon his arrival. Despite his intervention the two continue to argue on the way to the office, with Mickey rejoicing in the Doctor’s dilemma: “the misses and the ex”.
As they arrive at the office the Doctor ponders that the rats may have been food for something, and his fears are confirmed when he opens the door to discover dozens of giant bat creatures hanging from the ceiling. Upon seeing them Mickey runs, and the others follow. Once they are gone one of the creatures wakes up and screeches.
The Doctor and his friends arrive outside, realising now that the creatures are replacements for the school staff. The Doctor takes the oil sample Rose collected and tells the others they must return to the TARDIS to analyse it. Sarah however has another idea and runs over to her car. The Doctor follows and is overjoyed to discover another old friend – K-9 – stored in the boot.
He examines the somewhat battered canine computer whilst Sarah explains that the machine, which the Doctor sent to her as a gift, has broken and she cannot repair it. Rose and Mickey share their scepticism regarding the contraption whilst high above them on the school roof one of the bat creature watches them. It looks on as they close the boot of the car and prepare to leave, then flies of into the night.
Some time later that night the Doctor, Sarah, Rose and Mickey all sit in a café. The Doctor begins trying to repair K-9 whilst talking to Sarah about her life since they last met. Sarah insists she waited for him once he had left but he claims she didn’t need him, she has proved already that she can investigate things on her own and keep the spirit of their friendship alive. Remaining insistent, Sarah remarks that her life now could never compare to the one she had with him.
Outside, unbeknownst to the group in the café, Mr Finch and one of the creatures from the school watch the unfolding scene from a nearby rooftop. Back inside Sarah continues, claiming that the Doctor doesn’t understand the pain of being a friend of his, having to witness a life out amongst the stars then return to one on Earth whilst he continues. Although the Doctor claims she is doing well in life she still claims that he could have come back. The Time Lord claims he couldn’t return, but refuses to explain why. Sarah then tells him that when he dropped her back on Earth it wasn’t the right place. Instead of taking her to Croydon he took her to Aberdeen.
Suddenly K-9 whirs to life. With Mr Finch still watching from the roof the Doctor rejoices as the computer recognises him. He hands over the sample from the kitchen, which is identified as Krillitane Oil. The Doctor explains to his friends that the Krillitanes are a composite race; they invade planets and then adopt the physical aspects they admire of the races they conquer before promptly destroying them.
The group then go back outside, where Mickey is distressed to discover several similarities between K-9 and himself; they’re simply there to help the Doctor when they are needed. As the Krillitane with Mr Finch grows restless, Rose enters a heated conversation with the Doctor, worried that she will be left alone in the future, as Sarah has been. He insists he will not leave her behind and finally explains why he finds it so difficult to confront his old friends – it is too painful for him. He tells her that because of his long lifespan he meets a great many people, but none of them can last forever. Whilst he lives on he must witness the ones he loves decaying and dying. Although Rose could spend her entire life with him, he cannot spend all of his with her. This, he claims, is the curse of the Time Lord.
Finch hears this and is surprised yet content to discover the Doctor is a Time Lord. His companion then swoops down, heading toward the four people below. It does not attack; instead it flies back up into the sky and away into the night.
The next day the Doctor, Sarah, Rose and Mickey return to the school. Rose and Sarah take the Sonic Screwdriver and head toward the computer lab to examine the hardware, the Doctor decides to confront Mr Finch, and Mickey is left to sit in the car and look after K-9.
Moments later the Doctor and Mr Finch arrive beside the school swimming pool, staring at each other from opposite sides. The headmaster introduces himself by his true name – Brother Lassar. The Doctor notes that Finch has kept his human form whilst the other Krillitanes now resemble bats, and Finch claims it is a personal preference. The others simply revert to human form when required.
The Doctor demands to know what the Krillitanes are planning; having assumed it is something to do with the children in the school. Finch tells him to figure out the plan for himself and prove his intelligence. The Doctor warns him that if her does not agree with what they are doing he will stop them. Finch seems surprised by this threat but the Doctor insists he will only warn the Krillitanes once. He claims he is no longer a young man, and his mercy is waning. Finch maintains the Doctor will not fight the Krillitanes, stating that soon he will join with them.
Meanwhile, Mickey sits alone in the car, frustrated at being left out and perplexed that he has only a metal dog for company. Elsewhere Rose and Sarah make their way to the computer room and again begin arguing again. Sarah insists she has no intention of continuing her travels with the Doctor, but recounts how difficult life can be without him. Rose continues to make caustic remarks and Sarah takes exception. Soon they compete over which of them has seen the most impressive sights with the Doctor and Sarah appears to win, revealing that she has encountered the Loch Ness Monster.
Soon the two laugh at their childish attempts at one-upmanship and instead share their experiences of being with the Doctor. They relate to his rushed explanations of things and his intimacy with the TARDIS, which causes them both to laugh. Moments later he enters the room, which prompts the pair to giggle even further.
Mr Finch meanwhile has made his way to the staff room where he tells his disguised brothers that they must initiate the final phase of their plan, claiming the day has come when they shall become gods.
Outside on the playground the children are hushed by a loudspeaker system, which announces lessons are to resume earlier than usual. The pupils cheer and run inside, all except Kenny who realises something is wrong with he classmates. The speaker also tells the remaining members of staff to return to the staff room, where Mr Finch and his fellow Krillitanes are ready to strike…
The students try to access the computer room but are turned away by Rose. The Doctor continues trying to open up one of the computers but realises it is protected with a deadlock seal, which his Sonic Screwdriver is unable to penetrate.
Whilst students are led into other computer rooms, under the watchful eye of Kenny, Mr Finch returns to his office and instigates a full lockdown of the school. Back in the computer labs the Krillitane teachers initiate the alien programme once more and the pupils begin typing, showing no signs of reluctance or questioning. Seeing this, Kenny runs to find help but finds all of the doors and windows locked.
In the empty computer room the Doctor watches the program as it runs, and realises it is some sort of code. Suddenly it dawns on him what the Krillitanes are doing – they are trying to solve the Skasis Paradigm, something that will enable them to achieve god-like abilities. With such power they will be able to posses the very building blocks of life itself. Outside, Mickey sees Kenny banging on the front door of the school and realises he must try and help the trapped boy. After consulting K-9 he decides upon a plan of action and tells Kenny to stand aside.
The Doctor explains that the Krillitanes have been using the heightened imagination of the children to solve the Paradigm, and have used the Krillitane Oil to amplify their intelligence. Mr Finch enters and defends his race’s lust for power, claiming they will change the universe for the better. He tries to tempt the Doctor to join their cause, stating that with the power they will soon inherit he would be able to prevent the Time War from ever occurring and thus save his people. He seems enticed by this prospect but Sarah cuts in, claiming he must accept that everything has its time and everything ends, the universe moves on and he cannot change that. Suddenly the Time Lord comes to his senses and flees with Sarah and Rose.
Elsewhere, Mickey starts the car and drives it through the front doors of the school, breaking the security lockdown. He clambers out and runs with Kenny to save the others. Meanwhile, in the corridors of the school Mr Finch stands alone, screeching. All over the building his fellow Krillitanes discard their human form and swarm the school.
Mickey and Kenny catch up with the Doctor, Rose and Sarah, who manage to escape to the canteen. There they come under attack from the Krillitanes but are saved by K-9, who blasts the creatures with his laser. The Doctor and his friends escape but the Krillitanes are soon hot on their heels. Emerging in an empty corridor the Doctor realises that having changed their bodies so much, the Krillitane’s oil is now poisonous to them, which explains the commotion in the canteen the previous day. He decides they must return to the kitchens and Kenny helps them on their way by smashing a fire alarm, triggering a noise loud enough to distract the bat-like attackers.
Whilst Mickey makes his way to the computer room to save the children, Mr Finch disables the fire alarm and again sets off after the Doctor, who has arrived back at the canteen. He tries to open a barrel of oil but, like the computers, it is deadlock sealed. K-9 arrives and claims he will be able to blast the barrel with his laser, but he will have to be in close proximity to the resulting blast in order to do so.
Back in the computer room Mickey unplugs the machines and the students are roused from their trance-like state. He tells them all to run and soon they are on their way to safety outside.
The Doctor says goodbye to K-9, realising he will not be able to escape in time. He then flees with Rose, Kenny and the distraught Sarah whilst K-9 assumes his position. Moments later the Krillitanes, now in human form, arrive and advance on him. He blasts the barrel, showering the creatures with oil. They writhe in agony and seconds later a blast rips through the school. Outside the children cheer. Rose and Mickey join them whilst the Doctor tries to comfort Sarah – apologising for what has happened to K-9.
Some time later Sarah arrives in a nearby park, where the TARDIS and the Doctor are waiting for her. He takes her inside and she marvels at the console room, commenting on how much it has changed since she last saw it. The Doctor offers her a place onboard when they leave but she declines, saying it is time she stopped waiting for him and got on with her life. Mickey on the other hand asks if he could come instead, and although Rose doesn’t seem too keen on the idea the Doctor agrees.
Sarah decides it is time to go, but before she leaves she tells Rose to come and find her if she ever needs help. Rose asks if she should stay with the Doctor despite knowing what might happen to her in the future, and Sarah tells her she must stay, claiming “some things are worth getting your heart broken for”.
She turns and goes outside, followed closely behind by the Doctor. After Sarah finally grasp the chance to say thank you for the time they spent together, the Doctor enquires as to her home life. She claims she has no partner; there was only one man for her, she travelled with him for a while but “He was a tough act to follow”.
After saying goodbye to her old friend Sarah asks that he do the same, even though he believes they will meet again. He looks at her and finally bids her farewell: “Goodbye…my Sarah Jane”. They embrace for once more and the Doctor returns to the TARDIS. However, he has one last surprise for his old friend. As the TARDIS fades from view Sarah discovers a newly repaired K-9 waiting for her. He trundles forward, greets his mistress, and together they walk off toward a new life…