Silence In The Library

The Doctor and Donna arrive in the 51st century at a planet-sized book repository simply called "The Library", summoned by an anonymous request for help on the Doctor's psychic paper. However, they find it completely devoid of humanoid life, and the Library's computers even claim as such, though when the Doctor widens the search for non-humanoid life, the Library's computers claim over "a million million lifeforms" exist. A Node, an information drone which presents a donated human face to the user to facilitate communication, warns them to count the shadows, which appear despite the lack of objects to cast them. As they try to search for answers, they meet a team of explorers, led by archaeologist River Song, who have come to ascertain the meaning of the Library's final communication, which states "4022 saved, no survivors". River Song seems to know the Doctor, has a diary with a cover matching the Doctor's TARDIS, and even possesses a sonic screwdriver. She also later displays knowledge of the TARDIS's "emergency programme one". She only admits that she will know the Doctor in his relative future, refusing to disclose more for fear of spoilers. Professor Song also recognises Donna's name, but avoids explaining why Donna was not present when she knew the Doctor.
The Doctor organises the team to make sure the area is well lit as he explains that they are surrounded by Vashta Nerada, microscopic carnivorous creatures that disguise themselves as shadows to hunt and latch onto their prey. He notes that they are usually nowhere near as aggressive or numerous as the ones here seem to be. Before he can fully explain, however, Miss Evangelista wanders off and is stripped to the bone in moments. The Doctor and Donna learn that the exploration team wears communication devices which link to their nervous systems for thought-based communication. As a side-effect, these devices tend to retain an imprint of the user at the moment of death, creating a short-lived "Data Ghost" of that person's consciousness, which is capable of communicating with the living (being 'unaware' that it is dead) but eventually dissipates to the point where it simply repeats the last thing it said or nonsense.
Curiously, the Library's operations seem to be tied to the imagination of a young girl; she sees the Doctor and Donna through the eyes of a security camera when they first break into the central room, the exploration team appears on her television when the Doctor attempts to hack the Library computers, and books fly from the shelves when she fiddles with the television's remote control. The girl is under the observation of Dr. Moon, a child psychologist, at the request of her father, but Dr. Moon insists to the girl that what she imagines in her nightmares is in fact real, while the real world is a lie. He also states that there are people in her library who need to be saved.The team's investigation is interrupted when a shadow of Vashta Nerada latches onto the pilot, Dave. Although the Doctor attempts to save him by sealing him inside his suit, the creatures manage to get inside, eat him alive, and then animate his suit in order to chase the other explorers. The Doctor attempts to teleport Donna back to the TARDIS while he leads the rest of the team to safety, but something goes wrong with the teleport and Donna fails to materialise properly. As the team races away from the possessed suit, the Doctor is horrified to find a Node with Donna's face on it, which claims that Donna has left the Library and has been saved. The show ends in a cliffhanger as the Doctor is forced to leave the Node behind, but is trapped by the approaching suit on one side and the Vashta Nerada shadows on the other.

The Unicorn and the Wasp

The Doctor and Donna Noble arrive in 1926 and are invited to attend a dinner party hosted by Lady Eddison and her husband, Colonel Hugh. They are thrilled to find one of the guests is Agatha Christie, and realize that today is when she will inexplicably disappear for ten days. As the party ensues, some of the guests are found dead, following patterns from Agatha's books, though the Doctor finds traces of alien morphic residue at one of the scenes. Donna also encounters a giant wasp, which she is able to scare off; as it flies off, it morphs into a humanoid shape and eludes her. The Doctor himself becomes poisoned with cyanide but his Time Lord physiology allows him to detoxify himself with a combination of ingredients and a "shock" provided by Donna kissing him. This inspires him to add pepper to the dinner meal; while harmless to humans, it would act as an insecticide due to piperine. As they eat, the guests hear the wasp sound, but the lights in the room are blown out before they discover the identity of the alien. When the lights are restored, they have found that Lady Eddison's Firestone necklace has been stolen, and that Roger, Lady Eddison's son, has been murdered.
The Doctor assembles the remaining guests in the sitting room, and first Christie, then the Doctor himself, reveal several truths they've recognized about the guests, including the identity of the thief who stole the Firestone. Most importantly, he has determined that Lady Eddison's claim of suffering from malaria years ago was due to her becoming impregnated by a Vespiform, who had also given her the Firestone necklace as a means of linking her telepathically with her child. Eddison ultimately left the boy for adoption. The Doctor reveals that child is the Reverend Golightly (Tom Goodman-Hill), and the murderer of the guests; his use of Agatha's works as means for murder was a result of his connection to his mother, who was reading one of Agatha's novels while the alien powers in Golightly manifested themselves for the first time in a bout of anger.Golightly reveals his alien nature, transforming back into a wasp and threatening the guests. Agatha grabs the Firestone necklace and lures the wasp away while driving towards the nearby Silent Pool, with the Doctor and Donna giving chase. When they catch up to Agatha, Donna grabs the necklace from Agatha and throws it into the water, the wasp diving in after it and drowning. However, due to her brief possession of the necklace, Agatha herself is lured to the water, but Golightly releases her from its possession before he dies, causing her to fall unconscious on land. The Doctor realizes this is the event that gave her the amnesia during her disappearance, and uses the TARDIS to quietly drop her near the Harrogate Hotel ten days later. As the two return to the TARDIS, the Doctor shows Donna that not only that Agatha's works will be remembered for a long time by producing one of her novels, Death in the Clouds, published in the year five billion, but that her amnesia may not have been complete, with wasps being a significant plot element of the work.

The Doctor's Daughter

Continuing from where "The Poison Sky" left off, the TARDIS kidnaps the Doctor and his companions Donna Noble and Martha Jones; and whisks them away to the planet Messaline, in the midst of a generations-long war between humans and the Hath, fish-like humanoids. Emerging from the TARDIS, Martha reveals that although she wanted to be home, she did miss the adventure. They are then met by armed men working for General Cobb. Cline, the leader of the men, forces the Doctor's hand in a progenation machine, using his DNA to create a soldier — Jenny, the episode's titular character.
Martha is captured by the Hath, and, following an explosion caused by Jenny, the Doctor, Donna, and Jenny are imprisoned by General Cobb because of the Doctor's pacifist attitude. Each of the primary characters learns about the war from its belligerents; the Hath and humans were initially meant to live in a peaceful colony, but were divided over a dispute about "the Source", believed by each side to be the breath of their creator. When the Doctor unwittingly reveals the location of the Source, the two sides race to claim it first. The Doctor, Donna and Jenny escape their prison cell when Jenny distracts Cline by flirting with him and holding him at gunpoint.
The Doctor is initially dismissive of Jenny but becomes closer to her as the episode progresses. Donna is also intrigued by a series of numbered plaques she notices in each room. When they reach the location of the Source, it turns out to be a terraforming device within a colonising spaceship. They discover that the plaques represent the date the building was completed, which was a mere seven days previous; the humans and Hath have bred so many generations through the progenation machines that their own history degraded into myth. The original casus belli was a power vacuum caused by the death of the mission commander.
Meanwhile, Martha has been making her own way to the Source via the surface with a Hath who dies saving her from quicksand; devastated she reunites with the Doctor and Donna near the Source shortly before both armies arrive.
The Doctor declares the war to be over, and releases the terraforming agent; everyone present lays down their weapons, with the exception of Cobb who tries to shoot the Doctor. Jenny steps in the way and takes a bullet to the chest. The Doctor cries as he holds her, lovingly telling Jenny they have many journeys to take as father and daughter. She replies she'd like to do that, and finally passes away. Enraged, the Doctor picks up Cobb's gun and holds him at gunpoint, to the shock of Martha and Donna, but refuses to shoot him. Angrily, the Doctor orders the humans and the Hath to build their society on the basis of 'the man who never would'.
With Jenny to be given a proper burial by Cline and the Hath, the Doctor takes Martha home. Martha says she can't handle the death and devastation any more and warns Donna that life with the Doctor can be dangerous. Donna nevertheless resolves to stay with the Doctor indefinitely. As Donna leaves them to walk on their own, the Doctor rehashes one of his lines from their time together ("We're making a habit of this"), while Martha expresses her sorrow about the Doctor losing Jenny. He remarks that there's always something worth living for before hugging Martha tightly and departing as Martha happily runs inside her home.
Concurrently, on Messaline, Jenny revives. She escapes Messaline, determined to follow in her father's footsteps by resolving disputes and fighting villains (and a whole lot of running).

The Poison Sky

Continuing the narration from "The Sontaran Stratagem", the Doctor and UNIT determine that the ATMOS automotive devices, Sontaran in nature, are creating a lethal gas that is slowly filling Earth's atmosphere. The Doctor and Donna Noble are inside in the TARDIS when the Sontaran clone of Martha Jones informs the Sontarans of its position, allowing them to bring it to their orbiting ship. The Sontarans then disable their teleport pods after informing child prodigy Luke Rattigan, their human agent in construction the ATMOS devices, that they never planned on taking him or his students off-planet and stranding him on Earth. Instructing Donna to stay inside the TARDIS, the Doctor learns that the Sontarans, led by General Staal are seeking to transform the Earth into a place hospitable to their species in order to clone more soldiers in their war against the Rutans. The Sontarans further prevent a launch of nuclear weapons by UNIT against their ship through the Martha clone; the Doctor, realizing that the Sontaran ship would be impervious to the weapons' impact, realizes the Sontarans are instead preventing the disruption of their atmospheric conversion.
UNIT attempts to attack the ATMOS factory, but the Sontarans use an energy field to cause the conventional copper-lined bullets in their weapons to expand and jam the firearms, leaving them helpless as the troops are decimated. UNIT re-engage in a counter-attack using non-metallic bullets, and along with the aircraft carrier Valiant blowing the lethal gas away, puts the Sontarans on the defensive. The Doctor cryptically relays instructions to Donna to re-engage the teleport pods while he goads Staal, and uses the distraction of UNIT's offensive to teleport to the factory and discover the real Martha in one of the Sontaran's cloning devices, deactivating her clone in the process. They return to the Sontaran ship to collect Donna and the TARDIS, and then return to Rattigan's estate, finding the teenager distraught over the potential disaster to Earth that he caused. The Doctor collects the necessary equipment to construct his own atmospheric converter, harmlessly igniting the poison gas across the globe and ending the threat. However, the Doctor is aware the Sontarans will not take their defeat easily and teleports with the converted aboard the Sontaran vessel, planning on activating it and destroying the ship. Staal calls the Doctor's bluff, knowing he would also die, but before anyone can react, Rattigan teleports aboard, forces the Doctor back to Earth, and sacrifices himself by triggering the device, destroying the ship and the Sontarans aboard.
As the ATMOS devices are removed from cars and destroyed across the globe, Martha says goodbye to Donna and the Doctor in the TARDIS and prepares to head home. However, before she can leave, the TARDIS suddenly springs to life, locking the doors and piloting itself to an unknown destination as the jar containing the Doctor's severed hand bubbles.