The young woman joins the other soldiers in defending the area as the Doctor explains that the machine his hand was in takes a tissue sample and grows it into a human being. Suddenly the soldiers are under attack from a race known as “the Hath”, humanoid creatures with faces like fish and whose speech is governed by a small tank of green bubbling liquid attached to their heads.
A gunfight ensues and the Hath abduct Martha. The Doctor tries to intervene but is stopped when his newly born daughter detonates a series of explosives and seals the tunnel. The Time Lord vows he will find his lost friend but is stopped when one of the younger soldiers, Cline, aims a gun at him. Confused that the Doctor and Donna have no weapons or intention of fighting, he decides to take them to his commanding officer, a man named Cobb.
On the other side of the blockade Martha is still alive and unhurt. She finds an injured Hath and examines him, determining his shoulder to be dislocated. The other Hath train their guns on her but she proceeds to put the shoulder back in place, an act of kindness that wins her the loyalty of the alien creatures.
Elsewhere, Donna introduces herself to the Doctor’s new daughter, who claims she has no name herself because it has not been assigned. She claims the only thing she knows is how to fight, and the Doctor identifies this as a result of being a Generated Anomaly. This term leads Donna to suggest the name Jenny for the young woman and she adopts it. The Doctor refrains from acknowledging Jenny as his real daughter, claiming she was systematically force-cloned from his tissue.
The Time Lord changes the subject and asks Cline the name of the world they are on. He tells him it is what is left of the planet Messaline. The small group emerge in a building that was once a theatre, now it is a shelter for soldiers. They are introduced to General Cobb, who dismisses the Doctor and Donna as peacemakers, whom shall be ignored for the good of ‘the fight’. He refuses to let them search for Martha, claiming all movement will be regulated.
Arriving at the Hath base Martha discovers identical cloning technology to the machine that created the Doctor’s daughter. She finds herself surrounded by Hath, but they do not seem interested in harming her.
Cobb tells the Doctor that at the dawn of Messaline’s existence the ancestors of his people arrived to build a new world, and started by carving out living areas beneath the planet’s surface. However, their dream of a new life died when they were apparently betrayed by the Hath, who were meant to be their allies.
Donna examines one of the rooms and questions why, if buildings must be forged underground, should they have windows. She also notes a strange metal plaque attached to the wall, on which is written a number.
The Doctor asks how long the war has lasted and Cobb tells him it has endured many generations. Jenny explains that all children of the cloning machines are born with the knowledge that the Hath are their enemies and they must be destroyed. Everyone lives to fight, and the only way out is death.
Back at the Hath base Martha examines a map of the underground complex. The Doctor finds a similar map in the human base and decides he must use it to determine the whereabouts of his lost friend.
Cobb, meanwhile, recalls the other mission of his people – to find the ‘Source’, a legendary object, said to contain the sigh of a great creator, who breathed life into the universe. It was lost when the war began but now both sides wish to find it, for whoever holds it controls the destiny of the planet.
Still examining the map the Doctor discovers a suppressed layer of information – a section that is missing. Cobb realises the Source must be concealed there and determines to find it so peace can be restored. The Doctor claims peace could be achieved by ending the war but Cobb claims it will only be achieved with the genocide of the Hath.
The Doctor continues to protest and Cobb places him and Donna under arrest. Jenny is taken as well as it is feared she may harbour the same feelings as the Doctor. Cline holds them at gunpoint and takes them away.
Elsewhere the Hath also prepare to move out and search for the Source, the hidden area of the map having been made available to their scanners as well. As they begin arming themselves Martha worries that she may have just started a war by accessing the map…
The Doctor, Donna and Jenny are locked in their cell. Donna discovers another metal plaque on the wall, also with a number etched into it. The Doctor begins considering the Source, and tells Jenny that the creation story of a god-like figure that breathed life into the world is just a myth. The Source may be real but it doesn’t contain cosmic breath – it could be a weapon, and he has shown Cobb and his soldiers how to get hold of it. He realises he must break out of prison, find Martha and then stop Cobb.
Jenny is astounded that a man who won’t call himself a soldier would confess to such strategic planning, but her would-be father claims he is doing so to stop the fighting. She retorts that that is the aim of every soldier and is surprised even more when the Doctor appears to produce a weapon. It is in fact his Sonic Screwdriver, which he uses to upgrade Donna’s phone so that it will be able to function away from Earth.
He calls Martha and she explains that the Hath are marching off to examine the area on the map the Doctor discovered, and the Time Lord realises that he may now have caused a bloodbath. He warns Martha not to leave the Hath base but the phone line is cut off.
Across the complex the Hath and their opponents, led by Cobb, all begin preparations to search for the Source. As dawn approaches, both sides arm themselves and begin moving out.
In their cell the Doctor hears the chant of the soldiers as they prepare to leave, and claims they must act quickly. Jenny offers to knock out their guard but the Doctor stops her. Again he tries to deny being her father but Donna is determined to make him see sense. She takes the Doctor’s stethoscope and holds it to Jenny’s chest. The Doctor listens as Jenny’s two hearts beat, and is silenced.
Donna claims Jenny is a Time Lord but the Doctor insists she is an echo of something that was far more than she was. He tells her that the entire race is gone now, consumed by a war. Jenny realises that the Doctor really is a soldier; he fought and killed for his people. Once more she claims that he is not so different than her.
Martha tries to find some way of recharging her phone, which is out of power. She decides she must go to the site of the Source as well, but she will be able to do so quicker than the others if she goes over the surface. A Hath soldier accompanying her warns her not to but she claims she will be safe from any dangers outside as long as she is quick in her journey. She prepares to leave but she is not alone, her new Hath friend decides to assist her.
Back in the cells Jenny distracts Cline, their guard, and manages to steal his gun. She forces him to free them and the trio leave. The Doctor manages to distract another guard with the use of a clockwork mouse, but Jenny decides to render him unconscious instead. Disgruntled by this, the Doctor orders her not to move and goes off to find a copy of the map of the underground complex.
Meanwhile, the Hath continue to march and Martha begins her ascent to the surface. Her Hath companion hesitates but ultimately decides to follow her. They emerge on a dark windswept wasteland, which they immediately begin to transverse.
Cobb arrives in the prison area and finds Cline tied up. He has his men free him before ordering that they all arm themselves for the journey to find the Source. He vows that having waited a lifetime to find the oracle, he will not let someone like the Doctor stop him achieving his goal.
Now exploring the base for themselves, the Doctor, Donna and Jenny find themselves in a tunnel hidden from the main map. Donna sees another of the number written on the walls and begins recording them down in a notebook given to her by the Doctor, who is now concerned with fixing a nearby control panel.
Jenny enquires as to the meaning of the Doctor’s life and Donna claims that he travels the universe fighting off aliens, saving planets, and running a lot. Jenny seems intrigued by this but their conversation is ended when a section of the tunnel wall slides away – the Doctor has discovered what he was looking for.
They disappear into the new tunnel whilst elsewhere in the base Cobb’s men are on the march. The trio turn a corner and find themselves confronted by a corridor guarded by laser beams, which the Doctor tries to disable. Donna finds another of the numbers she has been recording and notes that each one is exactly the same length, but the value of each decreases with every new plaque.
Jenny hears General Cobb approaching and prepares to shoot them down. The Doctor stops her, and tells her that she must stop killing because soon it will infect her and she will never be able to keep her conscious clear. She disobeys him and proceeds to open fire on the approaching soldiers.
The Doctor and Donna manage to disable the lasers and proceed down the corridor, the Doctor still angered that Jenny craves the life of a soldier. At the other end of the passageway Cobb tries to persuade Jenny to join his battalion and defeat the Hath, but she refuses and aims her gun at him.
However, instead of killing him she shoots a pipe above his head and steam pours out, creating a barrier between them. She runs to join the Doctor and Donna but when she arrives the lasers power up again and stop her from proceeding. The Doctor confesses he cannot break the circuit again from his end of the corridor, but Jenny has her own way of getting past the lasers. She leaps forward and flips over them like a gymnast, managing to jump effortlessly past each one until she is with the Doctor and Donna at the other end. She tells the Doctor that she was unable to kill General Cobb, she had a choice, and she chose not to. The Doctor smiles.
Cobb arrives at the end of the corridor and the Doctor warns him that if the Source is a weapon he will not let him use it. Cobb retorts, claiming either man will die today and he will not let it be himself. He shoots but the Doctor escapes.
Above ground Martha and her Hath friend continue their journey. Suddenly Martha looses her footing and plunges down a slope into a bog, where she begins sinking. The Hath accompanying her leaps in and pushes her to safety, but is unable to save itself. Martha looks on as her saviour drowns and begins crying, alone on the windy landscape.
Jenny continues to ask the Doctor and Donna about travelling, and Donna claims it is an ever-changing lifestyle that both of them enjoy. Donna hints that Jenny might see a few new world of her own, and the Doctor admits that he will take her with him in the TARDIS, because he doesn’t want to leave her alone on Messaline.
Excited by this, Jenny runs on ahead and the Doctor is left to tell Donna that the reason for his initial reluctance to accept Jenny is because when he looks at her he sees the family he lost before – the family he has come to realise he will never see again. Donna tells him something she has never said before – she believes him to be wrong. Gunfire signals that Cobb and his men have passed the laser beams, and the duo, along with Jenny, begin to run.
Outside, Martha struggles on and discovers what she has been looking for – a giant tower reaching up into the dark sky.
The Doctor, Donna and Jenny find themselves at what appears to be a dead end, but the Doctor is convinced it is the entrance to the temple containing the Source. He begins trying to open up a nearby door whilst Donna examines another of the numbers written on a nearby wall.
As Martha arrives inside the tower the Doctor and his friends also make their way into the ‘temple’, which they discover is in fact a space ship. Donna assumes it to be the one the first settlers arrived on but the Doctor claims if it were it would not still be powered up and in such good condition.
Soon the Hath are beginning to break their way inside and General Cobb is leading the opposing assault force onward. The Doctor locates the ship’s log and discovers it is in fact the ship belonging to the original settlers. The original intention was to build a city using robotic drones, one in which humans and Hath could co-exist. However, the mission commander died and the settlers disagreed about who should take control, and split into two squabbling factions.
Donna sees another of the numbers, this time displayed on a computer screen. She realises the number is in fact a date, and each number written around the base is a completion date for the construction of the city. Her calculations would dictate that the base only a few days old – meaning the war began only a week ago. Because twenty new generations can be born in one day and many others can die at the same time (and pass on the legend of the war), the timescale of the conflict has been believed to be enormous when in fact it is very small.
The Doctor then notes that if the ship holds the key to understanding the people of Messaline then the Source must be part of the mystery as well. They hurry to try and find it and meet Martha on the way, who has noted the small of flowers in the air.
The race to find the Source continues and the Doctor finds himself emerging in a wide-open area populated by vegetation. The Source, a glowing orb of energy, sits in the middle of everything and at last the Doctor understands what it is – a terraforming device in transit state.
The humans and the Hath arrive and the Doctor explains that the Source is meant to make the planet inhabitable for them both to live in. He takes the large orb, holds it up and then smashes it on the ground. The energy that escapes spreads out across the area and begins growing new life.
However, Cobb is not finished yet. Infuriated at the Doctor’s attempts for peace he aims a gun at him. Jenny foresees what is about to happen and leaps to her father’s aid, taking the bullet herself. As Cobb is restrained Jenny falls to the floor and the Doctor takes her in his arms. She marvels at the beauty of the new world growing around her and the Doctor tells her to be strong – they have a life to live together. At last he accepts she is his daughter, but it is too late and she dies in his arms. He thinks for a minute and wonders if she will regenerate. Martha tells him there are no signs of life left; she was not enough like him. He retorts:
“No…too much. That’s the truth of it; she was too much like me.”
He lays her down and kisses her, then gets to his feet. He picks up a gun and aims it at Cobb’s head, threatening to kill him. He thinks for a moment, wild with rage, but then he stops. He throws the weapon down and confesses:
“I never would. Have you got that? I never would. When you start this new world; this world of Human and Hath, remember that. Make the foundation of this society a man who never would!”
As new life comes to Messaline, blowing away the dead soil outside so that light shines through the windows of the city, Cline prepares Jenny’s funeral ceremony. The Doctor, Donna and Martha return to the TARDIS, where the Time Lord explains that the reason the ship brought them to Messaline was because it sensed Jenny was there. However, it caused them to arrive before she was born – thus creating a paradox.
Soon Martha is returned home to face her new life. She talks with Donna about wanting to leave travelling behind, but the Doctor’s latest companion claims she will never return to normal life, she will travel forever. They wish each other good luck and Martha bids the Doctor goodbye once more, confessing that she though that Jenny would give him something to live for at last. The Doctor insists that he already has things to live for, even if there is much to die for as well.
Back on Messaline Jenny’s story is not over yet. As she lies in state golden streams of energy begin to flow from her mouth, and she is resuscitated. Alive once more she runs to a nearby shuttle and prepares to leave. Cline, who has been tending to her body, tells her to come back but she insists she has a universe to explore:
“I’ve got the whole universe. Planets to save, civilisations to rescue, creatures to defeat…and an awful lot of running to do!”
She flies off into space, in search of new adventures, just like her father.