James is furious with Eve when he realises she didn’t wait for him in the van. They watch as Katherine leads Tegan out of the bar at gunpoint, with the Doctor following close behind, protesting. Tegan suspects the Doctor must somehow be involved, and he’s surprised when Katherine says he‘s responsible for everything that‘s happening! They head towards James’s van and when Eve is ordered inside, they realise James is involved in the kidnap too. He wants Katherine to shoot the Doctor and when she hesitates James knocks the Doctor out with a single punch. Tegan and Eve are placed in the back of the van and the two kidnappers drive away.
Michael and Jodi leave the bar and find the Doctor recovering in the street. He asks for their help and they all climb into Michael’s car and head straight for Chambers Pharmaceuticals. As they drive through the streets, Michael blames the Doctor for Tegan being kidnapped and even he must admit that for some reason Dr Chambers seems to have a grudge against him. The Doctor realises from Michael’s demeanour that he and Tegan were involved in a relationship and he wonders whether they split up because of her brain tumour. This news is a shock to Michael who had no idea his former partner was ill.
James is celebrating the culmination of all their years’ work. Eve is furious at being caught up in something that doesn’t concern her, but James insists that she was part of their plan all along - in fact, she’s going to provide the cure they‘re looking for. They arrive at the surgery and Katherine goes in first to get everything set up. In the back of the van, Tegan tries to reassure the panicking Eve. James orders them out and tells them there’s someone he wants them to meet, and together they‘re going to change the world. Katherine goes up to the fourth floor where she promises someone she will save them…
Michael drives up to Chambers Pharmaceuticals and he and the Doctor formulate a plan for getting inside. Michael proposes getting a gun, whereas the Doctor is more interested in examining the advanced security system. Jodi believes she can switch off the security cameras if she can get inside first, but the Doctor doesn’t want her to go in alone. Jodi has Katherine’s telephone number (she admits that she deliberately organised Tegan’s surprise birthday party because she knew Tegan wouldn’t like it) so she rings it and demands money off the kidnappers in return for her silence. She asks to be let in to discuss terms. She heads off towards the building, leaving both the Doctor and Michael speechless.
Tegan and Eve are forced out of the lift by James and they join Katherine who tells them Jodi is asking for money. Tegan asks why they’re here and Katherine explains they’re looking for a cure, but not for her brain tumour. James brings out the real patient - her brother Nate. Tegan recognises straight away that the technology keeping the man alive is alien and Katherine explains that she’s met the Doctor before, but in a later incarnation. He left behind some alien equipment and she’s been experimenting with it for years in search of a cure for Nate. Katherine shows her the conversion device and Tegan realises in horror that her brother is becoming a Cyberman! Twenty years earlier she had given half the device to James, knowing he was good with computers, but she wasn’t sure she entirely trusted him, so she left the other half at home. Unfortunately it self-destructed and two people were killed. If she tells the Doctor now, perhaps he can stop it from happening in the future. Tegan knows from experience that he would never agree to change history, not even to save someone’s life.
Just before Jodi enters the building, she phones home and leaves a message for her family. The Doctor has a new respect for the young woman, although Michael still has a nagging doubt that she might genuinely be after the blackmail money. Michael wonders why Tegan never mentioned the Doctor before, but the Doctor counters this by asking him why Tegan never told him about her illness. Michael is convinced that Tegan still loves him and she broke up with him because she didn’t want to hurt him. Before long the two men are exchanging rather bitchy comments about which one of them was closest to Tegan and the Doctor lets slip that he’s a time traveller. Michael recalls a drunken conversation she had with Tegan a few years ago (the night he proposed marriage to her) in which she mentioned the fact that she knew a man once who changed her life and showed her the future. Until today, he dismissed this as the drink talking, but now he realises the truth. The Doctor is the reason Tegan wouldn’t marry him, the reason why Tegan is all alone. Did the Doctor never think that perhaps Tegan was in love with him…?
The Doctor is stunned by this revelation. Michael explains that Tegan tried to let go, but couldn’t - not even after throwing herself into running the company. It was as though she knew her life would never be that exciting again, so she blocked it out. Michael’s phone rings - it’s Jodi. She’s in the reception and she’ll leave the phone switched on so they can hear everything that happens. They listen as James greets her and then pulls a gun on her. She claims to have left instructions with a friend to call the police and tell them where she is if she doesn’t call them back in ten minutes. James is impressed, but not overly worried. He invites her into the lift and they go up.
Tegan wonders why Katherine is doing everything James asks, and she explains that they both have the same aim. Tegan wants to know more as she might even agree with what they’re doing. Katherine says Eve is the key to their plans - the moment she walked into their lives they knew they could succeed. It’s her mind they need and she’s going to be part of the System they’re creating.
James takes Jodi to his computer room which is filled with advanced technology. This is his System and everything in the building is controlled from here. James is an expert in computers and over the last couple of years he’s been going around repairing equipment all over the city - she recalls him fixing the computer server at Tegan’s company earlier that day - and now they all contain something extra that he’s devised. It means he can shut down every affected computer and phone line in the city at the press of a button. It will then act like a computer virus and spread to the entire communication network in Brisbane. Jodi sends a coded message to the Doctor and Michael asking them to create a distraction…
Katherine asks Eve if she ever wondered what it would be like to be more than just a receptionist? As a human being, she’ll die - but her soul will live on in the System. Tegan asks her if it’s fair to kill Eve just to save her brother, but she says it will save everyone. Just think…no more grief, no more funerals, everyone will live forever! Tegan punches Katherine and knocks her out, but as she and Eve try to escape the Nate/Cyberman steps forward and blocks their way…
The Doctor urges Michael to activate the burglar alarm on James’s van, but nothing seems to do the trick. He even tries to smash a window himself using Venusian Aikido, but he only succeeds in falling over! They hear James activate the signal that will switch off the computers and phones - and Jodi’s mobile goes dead. At that moment, the car alarm is activated and the Doctor and Michael take cover. Upstairs in the computer room, James looks out the window when he hears the alarm going off and Jodi uses the opportunity to switch off the security cameras. James turns his attention back to her and points out that with all the phones dead, no one can contact the police so her blackmail attempt has backfired. He lures her into the lift, then shoots her several times. Down on the ground floor, the Doctor and Michael have entered the building and are waiting for the lift when the door opens…to reveal Jodi’s dead body. Michael is devastated and suddenly realises this must be what the Doctor used to put Tegan through.
Tegan and Eve fight with the Nate/Cyberman until James returns and orders the creature away. Katherine recovers and Tegan is confused as to why they need her at all - they didn’t even know about her connection to the Doctor until today. James says everything will become clear shortly… The Nate/Cyberman grabs Eve and when Tegan tries to stop it, James threatens to shoot her. Eve is dragged away to be plugged into the interface. Katherine explains that the alien technology controls people, but it also helps them by revitalising them and keeping them alive. She and James have spent years trying to create a hospital that can diagnose all illnesses and cure them. The problem is that Cyber-technology needs a human component to control it. This will be Eve’s role.
The radio reports that the city’s telephone system has been hit by some kind of electronic attack. The entire network has gone down, causing disruption to many homes and businesses, and sparking fears of a terrorist attack. Despite pleas for calm, a number of incidents have already broken out…
The Doctor and Michael burst in, but it’s too late and Eve is connected to the System. The computer network activates and speaks in Eve’s voice. Katherine asks System to perform a self-diagnostic and she and James are delighted that their plans seems to be working. Tegan is devastated by the news of Jodi’s death and with Eve gone too, she blames the Doctor for bringing the horror back into her life. She reveals that he will meet Katherine in the future and he realises how complicated things are getting. Katherine joins them and announces that Tegan is to be System’s first test patient. She’s already discovered that Tegan’s tumour is alien in origin and has been growing inside her for over twenty years. It’s yet more evidence that travelling with the Doctor brings unacceptable risks. The Doctor wants to examine her himself, but Tegan refuses to be treated by either of them. She doesn’t want any more alien stuff in her head and she’s choosing to take her chances without medical treatment. She knows the Doctor was disappointed with how her life turned out, but she doesn’t think it’s been too bad. She’s been happy and she’s enjoyed having a normal life. When James returns, Katherine suggests the Doctor might actually make a better test study anyway. He knows everything, so they can get System to look into his mind. She knows he’s able to regenerate after death, so perhaps they can do more than just treat people - perhaps the can bring the dead back to life!
The Doctor can understand Katherine’s desire to create the ultimate medical computer, but he can’t understand why James is involved. He reveals that he works for an organisation that finds xenotechnology and makes use of it. System is his special project. The Doctor asks Katherine whether he’ll recognise her when he meets her in the past, but she’s fairly sure he didn’t. He himself is fairly confident that he wouldn’t have allowed what happened to Nate to happen if he’d been previously aware of it, which means that for some reason he’s going to forget everything. System orders the Doctor to be placed on a bed and it begins its examination. Overlooked by the others, Michael asks Tegan whether she ever loved him and why she didn’t tell him about her illness. She didn’t want to be treated as a victim, which is how the Doctor would have seen her.
The Doctor interfaces with System and learns that the Gathering has begun. He soon realises the computer includes a mixture of Cyber and Time Lord technology and he asks System to “fix” him so that when he next meets Katherine in the future, a trigger is activated that will remind him of what’s happened. It needs to be something he can mentally project to Kathy or anyone else, so System agrees to use make use of the Gallifreyan technology to boost his own telepathic ability. He suggests they use the name of the bar, 8687.
James and Katherine are impatient to see what information is being gathered by System and are surprised to discover the Doctor and the computer just seem to be talking. They interrupt System’s programme so that it can begin the examination proper, but the Doctor points out that he can shut down his entire body and die right there and then if he chooses. He makes it promise that no matter what else happens, it must find a cure for Tegan and make sure she’s safe. He tries to appeal to Eve’s nature within the computer, but there’s nothing left of her. The examination begins and Katherine is delighted by the amount of information being absorbed from the Doctor’s mind. James immediately starts making a backup of System. In the side room, the Doctor screams out in sheer agony and Katherine becomes concerned that they’re killing him. They realise this may actually be the moment when he changes into the new Doctor…
They’re interrupted by a scream from the room where Tegan and Michael were being kept. They switch on a monitor and see Michael panicking over Tegan’s motionless body. James doesn’t care as they no longer need Tegan’s input, but Katherine goes to investigate. She enters the room and is immediately overpowered by Michael and Tegan. They take her prisoner and order her back into the control room, but when they arrive they find James has gone and taken his backup of System with him. Tegan orders the Nate/Cyberman to free the Doctor or she will kill Katherine. The creature goes to the controls and releases the Doctor, who appears to be in a trance and is repeating the number ’8687’ over and over. He recovers and thanks Tegan for saving his life. She then orders the Nate/Cybermen to shut down System completely, but the Doctor asks her to let Katherine go free.
The Doctor tells Katherine that he’s seen all this before - it all starts when someone wants to cure one person, but then they realise they can make everyone better, stronger and fitter. Not just one person, they can improve on the whole of humanity. This is how the Cybermen were created. Although she’s trying to save her brother, there’s nothing left of him any more. If Katherine makes the choice to continue, it will be the last choice anyone will ever make - there’ll be no free will from that moment onwards. The world will just be one big logical machine. Tegan speaks directly to Nate and tries to persuade him that he should have died years ago. He saw what happened to his own father - is that what he wants to happen to him too? The Doctor joins in and points out that Nate himself is the one stopping his sister from getting on with her life.
The Nate/Cyberman initiates System’s self-destruct sequence. The Doctor urges everyone out, including the protesting Dr Chambers. They race out and get to cover just as the building explodes. Once they’ve established that everyone is alright, Michael wants to call the police, but the Doctor would rather take Katherine away as she needs help rather than punishment. He still can’t understand why he won’t remember any of this in his future, so he sends Tegan and Michael home and arranges to meet them the next morning.
The radio reports that Brisbane is returning to normal. The police say the breakdown of the city’s telephone and satellite systems was down to a minor technical fault and everything should be up and running within the hour. The explosion of Chambers Pharmaceuticals has been put down to a gas leak and two women are known to have died. They are named as Dr Katherine Chambers, but the identity of the second victim has not yet been revealed. The two incidents are not believed to be connected, but a terrorist attack has been ruled out.
Tegan and Michael wake up to the sound of the TARDIS materialising. She asks Michael to stay behind as she wants to say goodbye to the Doctor properly this time. Tegan greets her old friend with a warm smile. He tells her that Katherine will be looked after he told the police that she and Jodi died in the explosion. In the meantime they will continue looking for James Clarke who’s still in possession of the backup copy of System. The Doctor’s attention then turns to Tegan. She’s still dying and he wants her to come with him, but she refuses. She doesn’t know how long she has left but she’s back with Michael and she’s happy. The Doctor remembers something a little embarrassing and he nervously explains that Michael thought she was angry with him because she is, or was, in love with him. Tegan bursts out laughing! Michael is sweet, but sometimes he can be a bit dim and only sees things in black and white. No, she isn’t in love with the Doctor. She’s got a career and a stunning apartment, but she doesn’t want any more aliens in her life. He asks her to reconsider, but she points out that he has new friends now - Peri and Erimem. How would they feel if she turned up? She doesn’t regret leaving him for one minute. It was great at the time, but she’s happy being home and she hasn’t been holding her breath waiting for him to come back because, in a way, he never left. She was changed by her experiences with the Doctor and hopefully she’s a better person as a result. Thanks to him she’s enjoyed every minute of her life and she’s learnt to appreciate ’magic’. This time it’s the Doctor’s turn to laugh. She kisses him and they say their final goodbyes.
“It’s funny, you know, one minute you’re living your life, day in, day out, and you never really expect it to change that much. But then there’s this man, he’s called the Doctor. He’s, well, he’s magic. He turns up and then he turns your whole life upside down. And then, off he goes. And you have to make a choice - do I stay? Do I stay here knowing there’s all that out there, or do I step through those doors? Do I step into that old blue police box? It could be dangerous. It’ll definitely be terrifying. It won’t be dull though. So, do I go with him? Do I leave my whole life behind and go and see the stars? What do you think?”