After ‘meeting’ River Song and defeating the Vashta Narada, the Doctor and Donna try to relax on a crystalline planet. Donna stays at a hotel while the Doctor takes a train trip to see a waterfall. However, due to the outside atmospheric conditions being dangerous, the train is sealed off.
Unexpectedly, the train stops, the drivers are killed, and one of the passengers is possessed by a mysterious creature that repeats words, causing the other passengers to be paranoid, and afraid she’ll open the doors. However, the stewardess soon realizes the danger and takes the alien-possessed woman with her. The Doctor and the passengers survive, but are somewhat shaken.
Next, the Doctor and Donna visit a intergalactic bazaar. However, a strange insect attaches to her back, transporting her to an alternate universe where she was unable to save the Doctor during the Racnoss invasion, and he therefore died, setting off a series of events with the Earth getting attacked by aliens, many of the Doctor’s companions dying, and London becoming a dystopia. However, Donna has help-Rose Tyler, who is also in this strange universe. Turns out she’s been universe hopping, trying to locate the Doctor-and has only been able to do so because the walls between realities are becoming weak, due to some strange event. She eventually helps Donna break out of the alternate reality, and whispers two words to her.
The two words: Bad Wolf.
As Donna tells the Doctor of her strange journey and the mysterious blonde woman, the Doctor asks her what the words were. When she tells him, the Doctor immeadiatly panics and goes outside-just like before, the words are EVERYWHERE.
The Doctor returns to Earth-except Earth then vanishes! Turns out it’s being moved to the Medusa cascade, a massive nebula, along with several other planets. Rose then arrives in ‘our’ universe. Ready to face what’s going on, while the Doctor’s companions-Martha, Sarah Jane Smith, K-9, Captain Jack and the returned Mickey and Jackie-mobilize to try to find out what’s going on.
They’re brought together by Harriet Jones (who is unfortunately killed soon after). Soon, the culprits who have taken the Earth becomes apparent-The Daleks, who have somehow rebuilt their species.
Eventually, the Doctor is able to locate the Earth with the help of the intergalactic police known as the Shadow Proclamation, Donna’s ingenuity and the help of the companions. He soon discovers the culprit of the Daleks stealing planets and invading-Davros.
The Dalek creator was presumed dead after the time war, like the entire species, but the last Dalek from the cult of Skaro, Dalek Caan, managed to time travel into the war and rescue his creator (although it also drove Caan completely nuts and severely damaged his casing). Davros then used his own cells to cultivate new Dalek mutants and rebuild the Daleks once more. Davros’s plan is to use the planets’s alignment to power the cruciform, a massive weapon that will exterminate all non-Dalek life everywhere.
The Doctor quickly rushes back to Earth where he assembles his companions, and reunites with Rose. However, their reunion is cut short as the Doctor is shot by a Dalek.
Badly wounded, the Doctor then begins to regenerate….
….but he retains the same appearence and persona, as he is able to to funnel off some of the energy to his spare hand (from the sycorax invasion); hence able to heal himself without changing.
The Doctor and companions soon board the Dalek flagship, except for Donna who remains in the TARDIS, however, while trying to help the Doctor out, she accidentally activates the hand, which then grows into another Tenth Doctor (Although one with human DNA and some of Donna’s attitude)-and also Donna gains the Doctor’s knowledge and experience in turn.
The Doctor 2.0 and the new “Doctor Donna” board the Dalek ship, and manage to mess around with and defeat the Daleks. However, the newborn Doctor clone then destroys the Dalek race.
With Davros defeated and the Dalek threat gone, the TARDIS then tows the Earth home, with the Doctor utilizing the whole crew-companions and Doctor clone included to man the console (as TARDIS consoles were actually meant to be helmed by multiple time lords).
The Doctor then says goodbye to her companions. Sarah Jane returns to her adopted son, Luke. Jack returns to Torchwood. Mickey decides to return to his original universe, and Martha likewise returns to help UNIT out. However, the Doctor drops Rose and Jackie back in the alternate universe, along with the Doctor clone. He reason Rose can help him console the Doctor clone, and that the Doctor clone can love her in a way he can’t, since he’s half human and hence unable to regenerate. So Rose decides to stick around with the clone.
The Doctor and Donna then return to the home universe, where unfortunately, Donna’s new knowledge and time energy could prove fatal to her human body. The Doctor unfortunately is forced to suppress her memory of their adventures, effectively making it as if they never met from her POV.
He leaves her with her mother and grandfather, who promise to take care of her on the Doctor’s behalf.
The Doctor is once again alone-and sad.