Part 1: Apotheosis
The Doctor and Amy arrive at what is intended to be Wembley Stadium, 2030. In reality they are on board a large space station. They enter an abandoned laboratory, only to be attacked by a plague robot. It is destroyed by a group of nuns with guns: Mother Ivana, Sister Bridget, Sister Sophia, and Novice Konami, along with two others. After Bridget confirms that they are not "abominations", they are taken prisoner. Ivana explains their mission: To investigate the structure, which entered human space a year ago, is of alien origin, and is emitting exotic particles, and to find out what happened to the previous expedition, which disappeared without trace six months ago. The group move ahead to locate the station's command hub.
Amy talks to Konami, who explains that she joined the sisters of purity to protect mankind from "the abominations". They then find the source of the exotic particles, which the Doctor identifies as a primitive attempt at building a time engine. Two plague robots attack and kill one of the nuns. The others retreat into the next room, where the Doctor uses the station's control computer to over-ride the security protocols and deactivate the robots. Sister Sophia finds a group of skeletons which she believes to be what's left of the crew. However, the Doctor finds a fully-functional teleport, meaning the crew must have left. That leaves only one explanation; The skeletons are the the first expedition. Ivana says that it's impossible, as the bones had to be hundreds of years old, but the Doctor makes a groundbreaking discovery. He has stubble. The passage of time is being accelerated as an after-effect of the time engine going wrong. Time is progressing faster in some areas than others, and unfortunately for Novice Konami, she is stood in one of the faster areas. She has been aged so much that she can barely stand. A lizard runs over Amy's foot, and the Doctor and her give chase. The nuns follow them.
Outside, a jungle has grown, and the plants are growing before their eyes. The lizard has died of old age. Realising that time is running out and getting faster and faster, the Doctor offers to take the group back to the TARDIS. With Konami in need of help, Ivana agrees. Amy wonders where the jungle is coming from, and why the plants are becoming blue the closer they get to the TARDIS. The answer soon becomes clear. At the centre of the forest is the TARDIS, mutated, with Cosette, Margaret and a Shasarak trying to force their way out.
Part 2: Hybridogenesis
The TARDIS is caught in an accelerated time field. Amy sees Cosette and Margaret, who beg her to help them. The Doctor pulls her back as they coalesce into one enormous creature. The nuns shoot to kill, but it kills one of them and grabs Konami, absorbing her into itself. It separates from the TARDIS and walks away through the ship, pursued by the nuns. With the time field dissipated, the Doctor and Amy enter the TARDIS. He realises what has happened: The jungle outside is the one from planet Basingstoke, which infected the TARDIS, resulting it absorbing the Shasarak, Axos, Cosette and Margaret. The temporal acceleration allowed the absorbed life forms to evolve into an independent being which was then expelled by the TARDIS, finally disinfecting it.
Meanwhile, the three remaining nuns, Ivana, Sophia and Bridget, have the creature cornered. However, to escape harm, it dematerialises. Ivana orders Bridget to rig the time engine with explosives.
The Doctor lures the creature into the teleport using his sonic screwdriver. While he is distracted, the nuns catch up with him, and Ivana holds Amy at gunpoint, demanding that he tells her everything he knows about time technology. He makes the deduction that the nuns are fighting a war, and they were hoping to find something on the station to use as a weapon. He also realises that it's androids that they're fighting, for two reasons: When they first arrived they were checked to see if they were organic, and everyone in the group has been getting visibly older except Sister Bridget. Bridget kills Sister Sophia and is attacked by Ivana, who manages to sear off some of her fake skin, showing her true robotic face. The Doctor seals the door, trapping him, Amy and Ivana inside.
Outside, Bridget connects to the control computer. Ivana explains that she is a Galatean, a robot duplicate with delusions of divinity. Bridget reactivates the plague robots, and Ivana uses her last sonic grenades to destroy all of the ones in the room. However, Bridget has amassed a small army of robots outside the door, and they cannot use the teleport to escape without killing the creature, and Cosette, Margaret, the Shasarak, and Konami with it. As the robots begin to cut through the door, Amy is caught in an accelerated time field and ages dramatically.
Part 3: Time Storm
Amy looks for reassurance from the Doctor that the ageing can be reversed, but receives none. Mother Ivana, wishing for them all to escape using the teleport, threatens to kill the Doctor and Amy if they don't destroy the creature inside it. Amy stands up to her, but the confrontation is cut short as the plague robots blast through the door. Ivana, having rigged the time engine with explosives, threatens to destroy it if the robots come any closer. Bridget shoots her anyway, fatally injuring her, but Ivana still manages to trigger the explosion, telling her to go to hell.
The robots are blown away by the force, and the Doctor and Amy are forced to leave the creature behind and take shelter in the eye of the storm to avoid being aged to death. The jungle dies and the wind stops, allowing them to leave and make their way to the control room to see if they can still save the creature. However, they are captured by plague robots and taken to Sister Bridget. Now insane, she claims to have "seen the light" and that they have been blessed by a "divine incarnation". The teleport opens...
...and Chiyoko emerges. She greets the Doctor and Amy as the one who made her and the one who saved her life. Bridget hails her as flesh and machine combined, the ultimate expression of being, and Chiyoko destroys her and the robots with a wave of her hand. The Doctor offers her his help, but she says she doesn't need it, looking into all the potential pasts and futures, seeing all the wars and wasted lives. She finds it fascinating. The Doctor begs her to save Amy in return for her saving the creature in the teleport that became her, but she declines, instead dematerialising and saying goodbye.
The Doctor apologises to Amy for always letting her down, but Amy says it's her fault, and she should have stayed in the TARDIS. She dies in his arms. The Doctor refuses to accept that she is gone, and uses the body patterns still on Bridget's bio-scanner and the teleport to restore them to how they were when they first arrived. With the station about to explode, the Doctor and Amy teleport back to the TARDIS, and pursue Chiyoko through the vortex.
- Eleventh Doctor
- Amy Pond
- Mother Ivana
- Sister Bridget
- Novice Konami
- Sister Sophia
- Plague robots
- The Doctor references Star Trek twice.
- This story features the creation of Chiyoko, the disinfection of the TARDIS, and the introduction of the Galateans and plague robots, both of which feature in the next story.
- The end of this story leads directly on to the beginning of the next, The Child of Time.
- The Doctor mentions abandoning Amy on "that first night". (TV: The Eleventh Hour)
- When the TARDIS mutates, Cosette from COMIC: The Screams of Death, Margaret from COMIC: Do Not Go Gentle Into That Good Night, and a Shasarak from COMIC: Planet Bollywood all appear on the surface, having been shown touching the TARDIS and disappearing in their respective first appearances.
- Other characters and elements that return are Chiyoko, (COMIC: The Golden Ones, The Screams of Death) Axos, who is now a part of the mutated creature, (COMIC: The Golden Ones) and the jungle from planet Basingstoke, along with a lizard. (COMIC: Supernature)