The Doctor and Donna are on the planet Shan Shen, mixing with the locals. Donna wanders away from the Doctor to explore. A mysterious fortune teller tempts Donna with a reading. The fortune teller searches Donna's past for a single event, finally choosing a moment in June 2007, where Donna and her mother are in a car at a T-junction arguing about her future. Sylvia is trying to persuade Donna to turn right and ask businessman Jival Chowdry for a job; but Donna turns left to go to her planned temp job at H.C. Clements. As the fortune teller attempts to persuade Donna to turn right, something crawls onto Donna's back. Finally, under the fortune teller's persuasion, Donna turns right and alters the course of her life as well as the future of all existence.
It is Christmas Eve 2007, but in an alternate world where Donna, who now never worked for H.C. Clements, has never met the Doctor. The Racnoss Webstar attacks London, and is destroyed by the army, at a terrible cost: near an ambulance and a group of UNIT trucks, Donna overhears a UNIT officer telling someone that they found a body. The Doctor's body. As Donna walks away, a blond figure suddenly appears: the Doctor's former companion Rose Tyler comes running down the street and asks for information about the body that has just been bundled into the ambulance. Rose is stunned to hear that it was the Doctor.
In April 2008, Donna is fired from her job in the photocopying firm. Meanwhile, the Royal Hope Hospital is mysteriously transported to the Moon. When it returns, there is only one survivor: a medical student named Oliver Morgenstern, who relates the terrible events. As in the original timeline, the hospital had been moved by the Judoon and infiltrated by a Plasmavore. Sarah Jane Smith (at the hospital with her son Luke and his friends Maria and Clyde) attempted to fill the Doctor's role, and did manage to stop the MRI machine from irradiating the Earth--but, without the Doctor, the humans couldn't find a way back to Earth, and all suffocated. Medical student Martha Jones gave Morgenstern the last oxygen tank so that someone would survive to tell the story.
As Donna digests the terrible news, Rose reappears, and warns her to leave London for Christmas 2008.
Donna takes Rose's advice, and treats her mum and grandfather to a Christmas holiday in the English countryside. On Christmas morning 2008, they watch in disbelief as a replica of the Titanic is reported to be heading straight for Buckingham Palace. The three run outside and watch, horrified, as a mushroom cloud rises above London.
Like many other refugees from London (and southern England, which was irradiated), the Nobles are forced to move to Leeds, since nuclear radiation from the crash showered over London. They are allocated a house that is shared with two other families.
In 2009, The United States pledges to help Britain with monetary relief but must abandon the plan when their own crisis strikes: 60 million of their population are turned into Adipose. Since London no longer exists, Adipose Industries had targeted the USA.
Some time later, Donna finds soldiers gunning at cars when the Sontarans activate the ATMOS devices, covering the Earth with a poisonous fog. A soldier again notices something on Donna's back and holds her at gunpoint, but is released when nothing is apparently there. That night, Donna meets Rose for a third time. Rose explains that the Torchwood team, aboard the Sontaran ship, are trying to stop the catastrophe. Suddenly, the sky is cleared by an atmospheric converter. However Gwen Cooper and Ianto Jones had given their lives to achieve this, while Captain Jack Harkness has been stranded on the Sontaran homeworld.
Rose, who refuses to tell Donna her name and will say only that she has "crossed reality", tries to explain that Donna had saved the Doctor's life in an alternate timeline, though Donna insists that she had never met him. Rose warns Donna about the coming "darkness" that threatens every single universe. Donna tries to walk away, but Rose then tells Donna that she will have to go with her when she is ready and that she has three weeks to decide. Rose warns Donna that when she comes with her, Donna will die. Then she disappears.
Three weeks later, the genial Italian family in Donna's house is evicted as England is now "only for the English". Since the oceans are closed off, they must be taken to a "labour camp". Wilfred says "That's what they called them last time.", alluding to the concentration camps of World War II. Later at night, Donna and Wilf talk about recent events. He notices that the constellation of Orion has gone, though there are no clouds. As the stars disappear throughout the sky, Donna realizes that Rose must be correct. She finds the younger woman, and tells her that she is ready.
Rose takes Donna to a UNIT base and shows her the TARDIS - salvaged from beneath the River Thames - which is dying following the Doctor's death. Using technology researched from the TARDIS, Rose switches on a light which reveals what is on Donna's back: a 'Time Beetle'. Rose explains that it "feeds off time by changing time" and that it is in a state of temporal flux and cannot be removed. Rose goes on further to state that Donna herself is also in a state of flux and has been since her birth. Donna is horrified and the light is turned off. In order to set things right, they prepare to send Donna back in time to stop her past self from turning right. Donna agrees to go, and is elated by the belief that rather than dying, "this whole world [will] blink out of existence [but] a better world takes its place." To this Rose remains silent.
Donna successfully lands back in June 2007, but realizes that she is a half a mile away from her past self and has only got four minutes to save the world. She tries to run to herself, but realizes that she will not make it in time. Donna realizes what Rose meant about her death and throws herself in front of a van; the fatal accident quickly causes a traffic jam that prevents Donna's past self from turning right. Right before she dies, Rose appears and whispers something into Donna's ear to tell the Doctor.
As the original timeline reasserts itself, Donna regains consciousness in the fortune teller's stall on Shan Shen. The frightened and baffled fortune teller flees, saying that Donna's will was "too strong."and first saying "what are you?", but then screaming "what will you be?!". The Doctor enters and an emotionally spent Donna collapses into his arms.
Upon examining the beetle, The Doctor tells Donna that it is part of the Trickster's Brigade and that normally it affects one person and the universe compensates (as what happened to Sarah Jane Smith), but in Donna's case, it created a parallel universe. The Doctor then muses on all of the unique coincidences surrounding Donna: the fact that she had two parallel worlds that formed around her (this one and the one in the CAL computer) and the fact that he's met her and her grandfather twice. The Doctor concludes that they seem to be somehow linked. Donna tells the Doctor she is nothing special, but he counters saying that she's "brilliant". Hearing that trigger's Donna's memories of Rose on the parallel world and she starts to relate Rose's warnings to the Doctor. When asked if she remembered the blonde woman's name, Donna said she was never told it, but Donna does tell the Doctor the two words the blonde woman whispered into her ear: "Bad Wolf". Horrified, The Doctor runs out into the market square to see the words Bad Wolf everywhere; on posters pasted onto the walls, on the ceremonial flags hanging over the market, even on the TARDIS itself. Inside the TARDIS itself, the control room is glowing red and the Cloister Bell is ringing ominously. When Donna asks what's going on, the Doctor replies, "It's the end of the universe."